/usr/lib/R/site-library/PSCBS/NEWS is in r-cran-pscbs 0.63.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 2243 2244 2245 2246 2247 2248 2249 2250 2251 2252 2253 2254 2255 2256 2257 2258 2259 2260 2261 2262 2263 2264 2265 2266 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 2280 2281 2282 2283 2284 2285 2286 2287 2288 2289 2290 2291 2292 2293 2294 2295 2296 2297 2298 2299 2300 2301 2302 2303 2304 2305 2306 2307 2308 2309 2310 2311 2312 2313 2314 2315 2316 2317 2318 2319 2320 2321 2322 2323 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 2335 2336 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355 2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385 2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400 2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415 2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460 2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 2685 2686 2687 2688 2689 2690 2691 2692 2693 2694 2695 2696 2697 2698 2699 2700 2701 2702 2703 2704 2705 2706 2707 2708 2709 2710 2711 2712 2713 2714 2715 2716 2717 2718 2719 2720 2721 2722 2723 2724 2725 2726 2727 2728 2729 2730 2731 2732 2733 2734 2735 2736 2737 2738 2739 2740 2741 2742 2743 2744 2745 2746 2747 2748 2749 2750 2751 2752 2753 2754 2755 2756 2757 2758 2759 2760 2761 2762 2763 2764 2765 2766 2767 2768 2769 2770 2771 2772 2773 2774 2775 2776 2777 2778 2779 2780 2781 2782 2783 2784 2785 2786 2787 2788 2789 2790 2791 2792 2793 2794 2795 2796 2797 2798 2799 2800 2801 2802 2803 2804 2805 2806 2807 2808 2809 2810 2811 2812 2813 2814 2815 2816 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827 2828 2829 2830 2831 2832 2833 2834 2835 2836 2837 2838 2839 2840 2841 2842 2843 2844 2845 2846 2847 2848 2849 2850 2851 2852 2853 2854 2855 2856 2857 2858 2859 2860 2861 2862 2863 2864 2865 2866 2867 2868 2869 2870 2871 2872 2873 2874 2875 2876 2877 2878 2879 2880 2881 2882 2883 2884 2885 2886 2887 2888 2889 | Package: PSCBS
==============
Version: 0.63.0 [2017-06-27]
SIGNIFICANT CHANGES:
o Package now depends on R (>= 3.2.0) and Bioconductor (>= 3.1) packages.
NEW FEATURES:
o estimateDeltaCN() for PairedPSCBS gained argument 'flavor' and new estimator
`flavor = "delta(mode)".
o Added isLocallyPhased() for PSCBS.
CODE REFACTORING:
o Now package imports aroma.light instead of only suggesting it.
o Package tests no longer test against the deprecated lazy strategy of future.
Version: 0.62.0 [2016-11-10]
NEW FEATURES:
o Added normalizeTotalCNs() for PSCBS objects.
o REPORTS: Updated report template for PairedPSCBS object such that reports
are also generated from DH-only data, i.e. when there are no BAF signals
(which may happen with DNA-Seq data).
o Added splitters = TRUE as the default for setSegments().
CODE REFACTORING:
o CLEANUP: Minor internal cleanup and restructuring.
Version: 0.61.0 [2016-02-03]
SIGNIFICANT CHANGES:
o Package now requires R (>= 3.1.2) released October 2014, because of its
dependency on the listenv package.
NEW FEATURES:
o segmentByPairedPSCBS() gained argument 'rho' for paired PSCBS segmentation
on total CNs (TCNs) and decrease-of-heterozygosity signals (DHs) as an
alternative to for instance TCN and allele B fractions (BAFs).
BUG FIXES:
o Segmentation using futures where not fully reproducible when known segments
where specified. Fixed by changing how the random number stream is set and
used.
Version: 0.60.0 [2015-11-17]
NEW FEATURES:
o PARALLEL: Add support for parallel processing via futures by utilizing the
future package. Parallel segmentation over multiple chromosomes (or known
segments) done by segmentByCBS() and segmentByPairedPSCBS() is enabled by
future::plan("multicore").
o REPRODUCIBILITY: Whenever argument 'seed' is given, the L'Ecuyer-CMRG stream
is now used to generate random numbers. For backward compatibility with
other types of random number generators, don't specify argument 'seed' but
instead use set.seed() to set the seed before calling the method.
CODE REFACTORING:
o Bump package dependencies.
Version: 0.50.0 [2015-10-14]
SIGNIFICANT CHANGES:
o Now argument 'preserveScale' for segmentByPairedPSCBS() defaults to FALSE.
In the past the default has effectively been TRUE, but has given a warning
since v0.43.0 (June 2014) that it eventually will be changed to FALSE. Now
it will give a warning that it has changed, unless the option is explicitly
specified. This new warning will eventually be removed in a future version.
Version: 0.45.1 [2015-09-16]
NEW FEATURES:
o More informative error messages when append() for CBS or PSCBS fail.
BUG FIXES:
o segmentByCBS(, ..., w, knownSegments) would give internal assertion errors
if one of the priorly known segments would have zero data points. Thanks to
Kirill Tsukanov (Moscow) and Eric Talevich (UCSF) for reporting on this.
Version: 0.45.0 [2015-09-11]
SIGNIFICANT CHANGES:
o Package now requires R (>= 3.1.1) released July 2014. This allows us to use
BioC (>= 3.0) (October 2014).
NEW FEATURES:
o segmentByCBS() gained argument 'avg'.
o Add writeWIG() for CBS objects.
o pruneByHClust() no longer gives a message about method "ward" is now named
"ward.D".
o Added skip = TRUE to report().
BUG FIXES:
o plotTracks() for CBS ignored arguments 'cex', 'col' and 'meanCol' if two or
more chromosomes were plotted.
o joinSegments(), resetSegments() and pruneBySdUndo() gave errors for multi-
chromosome (>= 2) segmentation results.
o segmentByCBS() would ignore argument 'w' (weights) if more than one
chromosome was fitted.
o tileChromosomes() for CBS returned incorrect locus data.
o gapsToSegments(gaps) gave an error if nrow(gaps) == 0 or contained no
'chromosome' column.
o findLargeGaps() could return NULL. Now it always returns a data.frame.
o The report() RSP-embedded TeX templates for CBS and PairedPSCBS data did not
escape sample and data set names to LaTeX in all places needed.
CODE REFACTORING:
o ROBUSTNESS: Package test coverage is 62%.
o ROBUSTNESS: Explicitly importing core R functions.
Version: 0.44.0 [2015-02-22]
o Package now requires R (>= 3.0.3) and BioC (>= 2.13), which are from March
2014 and are in fact old. It's recommended to use a more recent R version.
DEPRECATED AND DEFUNCT:
o CLEANUP: bootstrapDHByRegion() is defunct (was deprecated since 2013).
CODE REFACTORING:
o ROBUSTNESS: Package test coverage is 58%.
o ROBUSTNESS: Forgot to declare some S3 methods in NAMESPACE.
o SPEEDUP: Now using more functions of matrixStats.
Version: 0.43.0 [2014-06-08]
SIGNIFICANT CHANGES:
o Now segmentByPairedPSCBS() gives a warning about future change of the
default value of argument 'preserveScale' (from current TRUE to FALSE).
The warning only appears if the argument is not specified explicitly.
o Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were released
April 2013 and are in fact old and it's recommended to use a more recent
version of R.
CODE REFACTORING:
o Now using use() of R.utils where possible.
o Bumped package dependencies.
Version: 0.42.2 [2014-05-24]
CODE REFACTORING:
o Bumped package dependencies.
Version: 0.42.1 [2014-05-05]
BUG FIXES:
o pruneByHClust() for PairedPSCBS would give an error on "unable to find an
inherited method for function 'anyMissing' for signature
'"PairedPSCNSegments"'", unless the object contained bootstrap statistics.
This is no longer needed. Thanks to Junsong Zhao, Los Angeles, CA for
reporting on this.
Version: 0.42.0 [2014-04-25]
CODE REFACTORING:
o Minor speedup (a few percents) by now byte compiling the package by default.
o CLEANUP: Dropped unnecessary usage of '::'.
o Bumped package dependencies.
Version: 0.41.4 [2014-03-30]
NEW FEATURES:
o GENERALIZATION: Now callROH() also works if paired PSCBS was done with only
'muN' available (and not 'betaN'). In that case, it assumes that all
genotype confidence scores are equal.
o Updated the ordering and the defaults of testROH() arguments to make it
clear that 'betaN' is optional and only used if 'csN' is not given.
o As an alternative to argument 'CT', segmentByPairedPSCBS() now accepts
arguments 'thetaT' and 'thetaN', in case 'CT' is calculated as
CT = 2 * thetaT / thetaN.
Version: 0.41.3 [2014-03-29]
NEW FEATURES:
o Methods no longer generates warnings on "in max(c(NA_integer_, NA_integer_),
na.rm = TRUE) : no non-missing arguments to max; returning -Inf".
BUG FIXES:
o In rare cases, callROH() could throw "Error in if (is.na(delta)) { :
argument is of length zero".
Version: 0.41.2 [2014-03-28]
NEW FEATURES:
o Added argument 'preserveScale' to segmentByPairedPSCBS(), which is passed as
is to normalizeTumorBoost() with the default being TRUE corresponding to the
previous default behavior.
Version: 0.41.1 [2014-03-28]
NEW FEATURES:
o Added unTumorBoost() to recalculating the segment means and other statistics
for a given PairedPSCBS profile based on non-TumorBoosted tumor BAFs (rather
than TumorBoost:ed tumor BAFs).
Version: 0.41.0 [2014-03-26]
NEW FEATURES:
o Now estimateKappaByC1Density() give more informative error messages if it
failed to identify modes for estimating the parameter.
o Added argument 'from' to estimateKappaByC1Density().
BUG FIXES:
o updateMeansC1C2() for PairedPSCBS did not handle missing values (=splitters)
in the 'c1c2Swap' field.
o updateMeans() for PairedPSCBS and NonPairedPSCBS returned the incorrect DH
segment levels for region in AB if adjustFor = "ab" and likewise for
segments in LOH if adjustFor = "loh". This bug does *not* affect any of
PSCBS methods themselves, because none of them utilizes those 'adjustFor'
options.
CODE REFACTORING:
o Bumped package dependencies.
Version: 0.40.4 [2014-02-04]
BUG FIXES:
o all.equal() for CBS would pass the first/dispatch argument to NextMethod()
as 'target = target' and not as 'object = target', which would result in it
being passed it twice both named and non-named where the latter would become
argument 'tolerance = target' in an internal call to all.equal() for
numerics. In recent R-devel version this would generate "Error in
all.equal.numeric(target[[i]], current[[i]], check.attributes =
check.attributes, : 'tolerance' should be numeric Calls: stopifnot ...
all.equal.default -> all.equal.list -> all.equal -> all.equal.numeric".
Version: 0.40.3 [2014-01-29]
NEW FEATURES:
o ROBUSTNESS: Now segmentByPairedPSCBS() asserts that argument 'muN' is not
all NAs. Similarily, if 'muN' is called from 'betaN' the same assertion is
done after calling.
Version: 0.40.2 [2013-12-17]
NEW FEATURES:
o Now estimateDeltaCN() for CBS have the option to estimate the size of a
copy-number unit based on the change-point magnitutes, in addition to the
estimator based on the density of segment means.
BUG FIXES:
o getChangePoints() for CBS returned empty results.
Version: 0.40.1 [2013-12-09]
DOCUMENTATION:
o The CBS vignette referred to C1 and C2 in one of the code examples.
CODE REFACTORING:
o Bumped package dependencies.
Version: 0.40.0 [2013-12-07]
CODE REFACTORING:
o CLEANUP: No longer a need for an ad-hoc NAMESPACE import.
Version: 0.39.8 [2013-12-04]
DOCUMENTATION:
o Now the vignette sections on dropping outliers before segmentation explains
why outliers are dropped whereas in the original CBS publication they were
shrunk ("smoothed"). Also, added help for dropSegmentationOutliers().
Version: 0.39.7 [2013-11-27]
NEW FEATURES:
o Added callGLAO() for CBS.
o Added encodeCalls() for 'data.frame' object returned by getLocusData(...,
addCalls = TRUE).
CODE REFACTORING:
o Bumped package dependencies.
Version: 0.39.6 [2013-11-23]
NEW FEATURES:
o Added clearCalls() for AbstractCBS.
o Added extractSegmentDataByLocus() for PairedPSCBS.
BUG FIXES:
o estimateDeltaCN() for CBS assumed aroma.light was attached.
Version: 0.39.5 [2013-11-15]
NEW FEATURES:
o Added estimateDeltaCN() for CBS. Added package system test.
Version: 0.39.4 [2013-11-14]
BUG FIXES:
o callGainsAndLosses() for CBS would not estimate the median median CN level
correctly if there were "empty" segments (e.g. gaps). This was/is due to a
bug in segments.summary() of the DNAcopy package. Instead, we are now
calculating the segment median levels ourselves. Added a system package
test for callGainsAndLosses().
Version: 0.39.3 [2013-11-05]
NEW FEATURES:
o Added basic implementations of setLocusData() and setSegments() for
AbstractCBS.
Version: 0.39.2 [2013-10-28]
NEW FEATURES:
o Now plotTracksManyChromosomes() for PairedPSCBS also supports tracks
"c1,c2", "c1", and "c2".
Version: 0.39.1 [2013-10-25]
NEW FEATURES:
o Now plotTracksManyChromosomes() uses the locus data field 'rho' when
plotting DH locus-level data. It only recalculates it from the tumor BAFs
if the DH signals are not available - if so a warning is generated.
BUG FIXES:
o The 'rho' signals returned by getLocusData(..., fields = "full") for
PairedPSCBS would have values also for homozygote SNPs.
Version: 0.39.0 [2013-10-23]
NEW FEATURES:
o Now all warnings generated by DNAcopy::CNA() are suppressed, including the
common one on "array has repeated maploc positions".
o Added getBootstrapLocusSets() for PairedPSCBS. Added a package system test
for it.
o Added argument 'subset' to applyByRegion() for PairedPSCBS.
o Added clearBootstrapSummaries() for PairedPSCBS.
o SPEEDUP: Added argument 'cache' to bootstrapSegmentsAndChangepoints(), which
caches the results to file if cache = TRUE.
Version: 0.38.6 [2013-10-20]
BUG FIXES:
o plotTracks() for PairedPSCBS would use argument 'Clim' for 'Blim' as well,
regardless of what argument 'Blim' is. This bug was introduced in v0.38.3.
CODE REFACTORING:
o Internal restructuring on how bootstrapping of segment means is done.
Version: 0.38.5 [2013-10-18]
BUG FIXES:
o The CBS and Paired PSCBS report templates assumed that the 'R.utils' package
is attached.
Version: 0.38.4 [2013-10-15]
CODE REFACTORING:
o CLEANUP: Removed a few unnecessary NAMESPACE imports.
o Bumped package dependencies.
Version: 0.38.3 [2013-10-14]
NEW FEATURES:
o Now plotTracks() for CBS and PSCBS gives a more informative error if 'Clim'
or 'Blim' is invalid. If using "auto" (only for CBS) and the limits could
not be inferred due to an unknown or unset signal type, an informative error
message reports on this as well.
CODE REFACTORING:
o Now the package vignettes are in vignettes/ and not in inst/doc/, which will
not be supported by R (>= 3.1.0).
o ROBUSTNESS: The overriding of append() to become a generic function does now
call base::append() in the default, instead of copy the latter. All this
will eventually be removed, when proper support for c, [, [[ etc. has been
added everywhere.
o CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
Version: 0.38.2 [2013-10-13]
BUG FIXES:
o While attaching the package, it could cause a cyclic loading of namespaces.
Version: 0.38.1 [2013-10-08]
NEW FEATURES:
o Now getSmoothLocusData() for CBS also returns column 'count' which specifies
the number of (finite) loci averaged over in each bin.
DOCUMENTATION:
o Vignette 'Total copy-number segmentation using CBS' would display the same
plot as vignette 'Parent-specific copy-number segmentation using Paired
PSCBS'.
o Renamed vignette 'Paired PSCBS' to 'Parent-specific copy-number segmentation
using Paired PSCBS'.
BUG FIXES:
o tileChromosomes() for CBS did not set "tiledChromosomes" attribute due to a
typo. This caused plotTracks() for CBS to horizontally misplace the plotted
segment levels. Added a system tests for this for CBS and PairedPSCBS
objects. Thanks to Ilari Scheinin at VUMC for reporting on this.
CODE REFACTORING:
o Bumped package dependencies.
Version: 0.38.0 [2013-09-27]
CODE REFACTORING:
o SPEEDUP: 'R CMD check' is now significantly faster due to copying of
pre-generated calculations ("memoization"). For instance, the the same
segmentation tests are roughly 40% faster compared to version 0.37.2.
o Now PSCBS imports 'R.cache' (used to only suggest it).
Version: 0.37.2 [2013-09-27]
CODE REFACTORING:
o SPEEDUP: Now utilizing 'matrixStats' functions in more places.
o ROBUSTNESS: Further improved how aroma.light is handled for backward
compatibility.
o Bumped package dependencies.
Version: 0.37.1 [2013-09-26]
CODE REFACTORING:
o CLEANUP: Now package avoids attaching suggested packages such as 'R.cache',
'aroma.light', and 'Hmisc' by only importing the set of functions needed via
'::'. This way those packages are only loaded. Packages that still need to
be attached are done so "quietly".
o CLEANUP: Minor adjustments to some of the internal workarounds for older
versions of 'matrixStats' and 'aroma.light'.
BUG FIXES:
o Forgot to import several functions from 'matrixStats'. These went undetected
because 'aroma.light' (<= 1.31.5) attaches the 'matrixStats'.
o segmentByPairedPSCBS() assumed 'aroma.light' was attached.
o One of the system tests assumed 'R.utils' was attached.
Version: 0.37.0 [2013-09-21]
BUG FIXES:
o WORKAROUND: For now, package attaches the 'utils' package. This is needed
due to what appears to be a bug in how 'R.oo' finalizes Object:s assuming
'utils' is attached, which may not be the case (unless 'R.oo' itself is
attached).
o callGNL() for PairedPSCBS used non-defined 'verbose' object.
CODE REFACTORING:
o CLEANUP: Package no longer attaches 'R.utils', only imports it.
o ROBUSTNESS: Now package imports only what is needed from 'DNAcopy'.
Version: 0.36.2 [2013-09-18]
DOCUMENTATION:
o Added vignette 'Total copy-number segmentation using CBS'.
o WORKAROUND: For R (< 3.0.0), hclustCNs() for AbstractCBS would generate
'Error in rowAlls(ok) : could not find function "loadMethod"'. This seems to
be a bug in R (< 3.0.0), which we can avoid by attaching the 'methods'
package in hclustCNs().
CODE REFACTORING:
o ROBUSTNESS: Now package imports 'matrixStats' (previously suggested).
o ROBUSTNESS: Now package declares S3 methods in the NAMESPACE.
o ROBUSTNESS: Package vignettes no longer assumes that the 'R.rsp' package is
attached.
o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().
o Bumped package dependencies.
Version: 0.36.1 [2013-09-10]
CODE REFACTORING:
o CLEANUP: Package no longer utilizes ':::'.
Version: 0.36.0 [2013-08-15]
NEW FEATURES:
o Made extractMinorMajorCNs() for PairedPSCBS acknowledge additional fields
related to (C1,C2).
Version: 0.35.6 [2013-08-01]
CODE REFACTORING:
o Updated the vignettes to utilize the new R.rsp features.
Version: 0.35.5 [2013-07-19]
NEW FEATURES:
o ROBUSTNESS: Added a sanity check on the estimates of (tauA, tauB) when they
are estimated from data in segmentByNonPairedPSCBS().
Version: 0.35.4 [2013-07-11]
CODE REFACTORING:
o Updated the Makefile for the vignettes and added .Rinstignore such that
auxiliary (bib and bst) LaTeX files are not installed but part of the build
so they are available to R CMD check, which is recently needed by R devel.
o Bumped package dependencies.
Version: 0.35.3 [2013-05-25]
CODE REFACTORING:
o Minor speedup by replacing all rm(x) with x <- NULL, cf. R-devel thread
'Assigning NULL to large variables is much faster than rm() - any reason why
I should still use rm()?' on May 25, 2013.
Version: 0.35.2 [2013-05-20]
DOCUMENTATION:
o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
Version: 0.35.1 [2013-05-07]
NEW FEATURES:
o Now estimateDeltaCN() for PairedPSCBS adjust for the ploidy if set.
o Added ploidy() and ploidy()<- for AbstractCBS.
o Now tileChromosomes() no longer gives warnings on "max(i): no non-missing
arguments to max; returning -Inf".
Version: 0.35.0 [2013-04-23]
NEW FEATURES:
o SPEEDUP: Now bootstrapTCNandDHByRegion() for PairedPSCBS always estimates
the default quantiles in addition to any requested ones.
o SPEEDUP: Made bootstrapTCNandDHByRegion() much faster by adding
use.names = FALSE to two internal unlist() statements.
BUG FIXES:
o updateMeans() for PairedPSCBS and NonPairedPSCBS could include a signal from
a neighboring segment when averaging, iff that signal was located at the
exact locus of the change point. Thanks Ingrid Lönnstedt (WEHI) for
reporting on this.
Version: 0.34.9 [2013-04-22]
BUG FIXES:
o updateMeans() would not always preserve the originally specified
segment-mean level estimator, if different from a (sample) mean estimator,
e.g. avgDH = "median". This could result in for instance callAB() failing
on internal sanity checks.
o Segment levels drawn by plotTracks() would have incorrect genomic locations
for chromosome 2 and beyond. This bug was introduced in v0.34.7.
CODE REFACTORING:
o Utilizing new startupMessage() of R.oo.
Version: 0.34.8 [2013-04-20]
DEPRECATED AND DEFUNCT:
o Removed previously deprecated methods for AbstractCBS.
Version: 0.34.7 [2013-04-18]
NEW FEATURES:
o Added more arguments to plotTracks().
o Now drawLevels() and drawConfidenceBands() for CBS and PairedPSCBS also
works for multiple chromosomes.
BUG FIXES:
o One of the system tests for segmentByPairedPSCBS() failed in the case when
the data was downsampled (in order to meet the CRAN requirements). The
workaround is to use a fix 'deltaAB' parameter in that case.
o Internal calcStatsForCopyNeutralABs() would give an error if there was
exactly two AB segments.
Version: 0.34.6 [2013-04-11]
BUG FIXES:
o plotTracks(fit, callLoci = TRUE) would color loci incorrectly if more than
one chromosome are plotted.
Version: 0.34.5 [2013-04-09]
NEW FEATURES:
o Now callROH() gives an informative error if called on a NonPairedPSCBS
object.
Version: 0.34.4 [2013-04-05]
NEW FEATURES:
o Added more end-user control to plotTracks().
Version: 0.34.3 [2013-04-04]
CODE REFACTORING:
o Now package builds with both R.rsp (< 0.9.1) and R.rsp (>= 0.9.1).
Version: 0.34.2 [2013-03-28]
NEW FEATURES:
o Now callGainNeutralLoss(), utilizes callCopyNeutral() by default.
Version: 0.34.1 [2013-03-21]
NEW FEATURES:
o Updated the report generator and its RSP templates.
DOCUMENTATION:
o Clarified in the PSCBS vignette that the NTCN caller is under development,
experimental.
CODE REFACTORING:
o SPEEDUP: Made dropChangePoints() faster by only updating the segment
statistics/means at the very end.
Version: 0.34.0 [2013-03-19]
NEW FEATURES:
o CALLING: Defined a formal hypothesis test for how segments are called copy-
neutral in TCN (NTCN), with the null hypothesis being that a segment is
NTCN. In order for a segment to not be NTCN, its confidence interval has to
be completely outside the null region. This changed how
callCopyNeutralByTCNofAB() for PairedPSCBS calls segments; it is now a bit
more conservative in rejecting NTCN.
Version: 0.33.4 [2013-03-19]
NEW FEATURES:
o ROBUSTNESS: Now calcStatsForCopyNeutralABs() for PairedPSCBS does a better
job in identifying the TCN mode of the AB segments.
o Added argument 'flavor' to findNeutralCopyNumberState() specifying how to
identify the main mode of the AB segments.
o VISUALIZATION: Now plotTracks() for PairedPSCBS displays thresholds for
calling AB, LOH and and NTCN.
Version: 0.33.3 [2013-03-12]
DOCUMENTATION:
o Documented 'tauA' and 'tauB' in the help for segmentByNonPairedPSCBS().
Version: 0.33.2 [2013-03-09]
NEW FEATURES:
o Added getLocusData() for PairedPSCBS and NonPairedPSCBS.
DOCUMENTATION:
o Updated the vignettes and the report templates to utilize the new ggplot2
themes - ggplot2 no longer gives a warning on using deprecated functions.
o Now report() for AbstractCBS also includes files listed in the optional file
'.install_extras' of the source RSP template directory. The same filename
is used by 'R CMD build/check' for including additional source files needed
to build the vignettes.
CODE REFACTORING:
o Added an Authors@R field to the DESCRIPTION.
Version: 0.33.1 [2013-03-07]
DOCUMENTATION:
o Preparing package vignettes for the upcoming R 3.0.0 support for non-Sweave
vignettes.
SOFTWARE QUALITY:
o Relaxed the internal precision tests of testROH(). This was done in
response to the CRAN farm lowering its precision on some hosts.
Version: 0.33.0 [2013-03-05]
NEW FEATURES:
o Added argument 'typeOfWeights' to estimateKappaByC1Density() for
PairedPSCBS, and hence indirectly to estimateKappa(). The default is
typeOfWeights = "dhNbrOfLoci", which may give too much overall weight to
very long segments causing the estimator to fail when there are only a few
number of "C1 = 0" segments. An alternative is to use
typeOfWeights = "sqrt(dhNbrOfLoci)".
Version: 0.32.6 [2013-03-04]
DOCUMENTATION:
o Updated the help usage section for all static methods.
Version: 0.32.5 [2013-02-09]
BUG FIXES:
o bootstrapTCNandDHByRegion() for PairedPSCBS did not bootstrap from all
available loci when calculating total CNs statistics, iff the segment had
been called run-of-homozygosity (ROH). Internal validation tests caught
this. Thanks to Oscar Rueda at the Cancer Research UK Cambridge Institute
for reporting on this.
CODE REFACTORING:
o Added a VignetteBuilder field to DESCRIPTION.
Version: 0.32.4 [2013-02-07]
NEW FEATURES:
o Improved some verbose outputs of bootstrapTCNandDHByRegion().
Version: 0.32.3 [2013-02-05]
NEW FEATURES:
o Now pruneByHClust() drops any existing segment calls and quantile mean-level
estimates.
Version: 0.32.2 [2013-02-01]
NEW FEATURES:
o Added resetSegments() for AbstractCBS, which drops extra segments columns
(e.g. bootstrap statistics and calls) except those obtained from the segment
algorithm.
DOCUMENTATION:
o Added a paragraph on avgDH = "median" to the PSCBS vignette's 'Experimental'
section.
CODE REFACTORING:
o ROBUSTNESS: Now aroma.light is explicitly required in cases where it is
needed.
Version: 0.32.1 [2013-02-01]
BUG FIXES:
o segmentByPairedPSCBS(..., avgDH = "median") only worked for single-
chromosome data. Same for avgTCN = "median". Thanks Ritu Roy at UCSF for
reporting on this.
Version: 0.32.0 [2013-01-16]
NEW FEATURES:
o Added arguments 'avgTCN' and 'avgDH' to segmentByPairedPSCBS().
o Now updateMeans() and updateMeansTogether() methods can estimate the mean
levels either by the sample mean or the median.
Version: 0.31.0 [2013-01-05]
CODE REFACTORING:
o CLEANUP: Now packages R.methodsS3 and R.oo are only imported.
o CLEANUP: Package no longer explicitly imports digest.
Version: 0.30.0 [2012-11-05]
NEW FEATURES:
o GENERALIZATION: Now bootstrapTCNandDHByRegion() works for more "flavors",
e.g the default ('tcn') used by segmentByNonPairedPSCBS().
Version: 0.29.9 [2012-11-05]
DOCUMENTATION:
o FIX: example(segmentByNonPairedPSCBS) was for the paired case.
CODE REFACTORING:
o CRAN POLICY: Further speed up of examples such that they run faster with
'R CMD check'.
Version: 0.29.8 [2012-11-04]
CODE REFACTORING:
o CLEANUP: Replaced all whichVector() with which(), because the latter is now
the fastest again.
Version: 0.29.7 [2012-11-03]
CODE REFACTORING:
o Updated deprecated ggplot2 functions in the RSP reports.
Version: 0.29.6 [2012-11-01]
CODE REFACTORING:
o Bumped package dependencies.
o CRAN POLICY: Made the examples run faster for 'R CMD check'.
Version: 0.29.5 [2012-10-16]
BUG FIXES:
o ROBUSTNESS: No longer passing '...' to NextMethod(), cf. R-devel thread
'Do *not* pass '...' to NextMethod() - it'll do it for you; missing
documentation, a bug or just me?' on Oct 16, 2012.
Version: 0.29.4 [2012-09-23]
NEW FEATURES:
o Now plotTracks() [and plotTracksManyChromosomes()] draws segment levels such
that it is easier to see them even when they are overlapping.
Version: 0.29.3 [2012-09-21]
NEW FEATURES:
o SPEEDUP: By default bootstrapTCNandDHByRegion() for PairedPSCBS no longer do
sanity checks within the bootstrap loop. This significantly speed up the
method. To run checks, use argument .debug = TRUE. In addition, the
callNnn() methods that need to call this method, does it by decreasing the
amount of verbose output substantially, which in turn speeds up the process
a fair bit.
o Now getSegments(..., splitters = TRUE) for CBS and PSCBS inserts NA rows
wherever there is a "gap" between segments. A "gap" is when two segments
are not connected (zero distance).
o ROBUSTNESS: Now append() for CBS and PSCBS drops column 'length' from
'knownSegments', iff it exists.
o Now nbrOfChangePoints() for AbstractCBS calculates only change points of
connected neighboring segments.
BUG FIXES:
o seqOfSegmentsByDP() for AbstractCBS would not handle empty segments, which
could occur if 'knownSegments' for instance included centromere gaps.
o segmentByCBS(... knownSegments) could return segments for chromosome 0 even
though it did not exist in the input data.
Version: 0.29.2 [2012-09-18]
NEW FEATURES:
o REPORT: Now report() for AbstractCBS looks for the RSP template in
templates/, and as a backup in templates,PSCBS/. If the latter does not
exist, it is automatically created as a soft link to templates/ of the PSCBS
package. This allows anyone to create their own customized copy (in
templates/) of the default PSCBS RSP report.
o REPORT: Now report(fit, ..., rspTags) for AbstractCBS looks for the RSP
template named <className>(,<rspTags>),report.tex.rsp, where className is
class(fit)[1] and argument 'rspTags' is an optional comma-separated
character string/vector. This makes it possible to have different types of
report for the same class of objects.
o REPORT: Added argument 'force' to report() for AbstractCBS. This will copy
the RSP template files again, although they are already in reports/ output
directory.
Version: 0.29.1 [2012-09-15]
NEW FEATURES:
o Added argument 'dropMissingCT' to segmentByPairedPSCBS().
Version: 0.29.0 [2012-09-14]
NEW FEATURES:
o Added trial version of pruneByDP() for AbstractCBS.
Version: 0.28.6 [2012-09-13]
NEW FEATURES:
o Now tileChromosomes() also adjusts 'knownSegments'.
o Added argument 'dropGaps' to gapsToSegments().
o Updated all.equal() for AbstractCBS to compare locus-level data, segments,
and other fields.
Version: 0.28.5 [2012-09-13]
NEW FEATURES:
o SPEEDUP: Now segmentByCBS(..., undo = +Inf) returns much faster, which is
possible because there is no need to identify new change points.
Version: 0.28.4 [2012-09-13]
NEW FEATURES:
o CONSISTENCY FIX: Changed the behavior of extreme values of argument 'undo'
to segmentByCBS() such that 'undo = 0' (was 'undo = +Inf') now means that
it will not ask DNAcopy::segment() to undo the segmentation, and such that
'undo = +Inf' means that no changepoints will be identified. The latter case
allows you to effectively skip the segmentation but still calculate all the
CBS statistics across a set of known segments via segmentByCBS(...,
undo = +Inf, knownSegments = knownSegments). Arguments 'undoTCN' and
'undoDH' to segmentByPairedPSCBS() are adjusted analogously. Corresponding
system tests were added.
Version: 0.28.3 [2012-08-30]
CODE REFACTORING:
o Updated code and Rd cross reference to use the 'matrixStats' package for
weightedMedian(), which used to be in 'aroma.light'.
Version: 0.28.2 [2012-08-20]
BUG FIXES:
o segmentByNonPairedPSCBS() forgot to specify namespace aroma.light when
trying to call findPeaksAndValleys().
Version: 0.28.1 [2012-08-15]
DOCUMENTATION:
o Minor grammatical corrections of the Paired PSCBS vignette.
Version: 0.28.0 [2012-07-22]
NEW FEATURES:
o Added argument 'minLength' to gapsToSegments(). The default is no longer to
drop zero-length (minLength == -1L) segments, because if (and only if) such
a segment contains a locus, then segmentByNnn() will currently generate an
(internal) error.
BUG FIXES:
o GENERALIZATION: Now segmentByPairedPSCBS() drops loci for which CT is
missing (regardless of betaT). For instance, in rare cases when the
reference (e.g. the normal) is missing, then it may be that CT is missing
while betaT is not.
Version: 0.27.4 [2012-07-22]
NEW FEATURES:
o Now verbose output of segmentByPairedPSCBS() specifies region ranges with
greater precision.
Version: 0.27.3 [2012-07-10]
DOCUMENTATION:
o Minor updates to the Paired PSCBS vignettes.
CODE REFACTORING:
o CLEANUP: One redundancy tests relied on a non-critical function that will be
removed in R.utils 1.16.0 (now in R.devices 2.1.1).
Version: 0.27.2 [2012-07-08]
CODE REFACTORING:
o Updated package dependencies.
Version: 0.27.1 [2012-07-02]
NEW FEATURES:
o Now we refer to "copy neutral" segments as "neutral TCN" segments with
acronym 'NTCN'. The corresponding column in the segmentation results are
labeled correspondingly. The Paired PSCBS vignette was updated accordingly.
Version: 0.27.0 [2012-06-24]
DOCUMENTATION:
o Some grammar corrections of the 'Paired PSCBS' vignette.
CODE REFACTORING:
o (An update that should be ignored)
Version: 0.26.1 [2012-06-05]
NEW FEATURES:
o Now segmentByCBS() for data frame:s does a better job identifying the CN
signals.
Version: 0.26.0 [2012-06-03]
NEW FEATURES:
o Now argument 'delta' for callCopyNeutralByTCNofAB() of PairedPSCBS is
calculated via estimateDeltaCN(), which estimates the width of the
acceptance regions, used for calling copy neutral states, to be a function
of the normal contamination.
DOCUMENTATION:
o Added details to the Paired PSCBS vignette on how to call segments that are
copy neutral (typically diploid).
Version: 0.25.3 [2012-06-03]
BUG FIXES:
o all.equal(target, current) for CBS objects would give an error if either
'target' or 'current' had zero segments.
Version: 0.25.2 [2012-05-30]
NEW FEATURES:
o Added writeSegments() for DNAcopy objects.
BUG FIXES:
o as.CNA() for DNAcopy added incorrect chromosome splitters.
o as.CNA() for DNAcopy would ignore argument 'sample' and always return the
first sample.
Version: 0.25.1 [2012-05-30]
NEW FEATURES:
o Now callROH() records parameter 'deltaROH' in the results.
DOCUMENTATION:
o Added details to the Paired PSCBS vignette on how to tune the various
callers.
BUG FIXES:
o callLOH(..., force = TRUE) would append multiple 'lohCall' columns, if
called multiple times.
Version: 0.25.0 [2012-04-20]
NEW FEATURES:
o Added a trial (very much true) version of segmentByNonPairedPSCBS().
Version: 0.24.0 [2012-04-20]
NEW FEATURES:
o Now it is possible to skip the DH segmentation in Paired PSCBS, i.e.
segmentByPairedPSCBS(..., flavor = "tcn").
Version: 0.23.2 [2012-04-20]
BUG FIXES:
o segmentByPairedPSCBS() would throw "error in `$<-.data.frame
`(`*tmp*`, "rho" ..." if some loci had unknown genomic positions.
Version: 0.23.1 [2012-04-20]
NEW FEATURES:
o Added RSP report for CBS objects (adopted from ditto for PairedPSCBS).
DOCUMENTATION:
o Updated the 'Paired PSCBS' vignette.
Version: 0.23.0 [2012-03-20]
DOCUMENTATION:
o Added a package vignette.
Version: 0.22.2 [2012-02-29]
BUG FIXES:
o plotTracks(..., add = TRUE) for PairedPSCBS would add TCNs when BAFs and DHs
were intended.
Version: 0.22.1 [2012-02-28]
o Updated package dependencies to R.rsp (>= 0.7.3) so that report() for
PairedPSCBS no longer require non-public packages.
NEW FEATURES:
o Now it is possible to turn off usage of the alpha channel in plots generated
by report(), which can be handy on systems where the default PNG device does
not support the alpha channel. Example:
setOption("PSCBS::report/useAlphaChannel", FALSE).
Version: 0.22.0 [2012-02-27]
NEW FEATURES:
o Added report() for PairedPSCBS.
Version: 0.21.0 [2012-02-27]
NEW FEATURES:
o Added argument 'fields' to getLocusData() for PairedPSCBS.
o Added renameChromosomes() to AbstractCBS.
Version: 0.20.0 [2012-02-26]
NEW FEATURES:
o Added alpha version of callGainNeutralLoss() for PairedPSCBS, which
certainly will be updated in the future. This caller is tested by the
system tests.
o Added dropChangePoints() for AbstractCBS.
BUG FIXES:
o extractSegments() for PairedPSCBS would return incorrect row indices, more
precisely, overlapping data chunks.
o bootstrapTCNandDHByRegion() for PairedPSCBS would resample from a subset of
the intended TCNs, iff the DH mean was non-finite while there were still
heterozygous SNPs. This introduced a bias in the estimates, which was
neglectable for large segments, but for very small segments (a few loci) it
could be relatively large.
SOFTWARE QUALITY:
o ROBUSTNESS: Added more sanity checks validating the correctness of what is
returned by extractSegments() for CBS and PairedPSCBS.
CODE REFACTORING:
o Added some internal utility functions for PairedPSCBS taken from the
aroma.cn package. Some of these may become public later, but for they
should be considered internal.
Version: 0.19.8 [2012-02-23]
CODE REFACTORING:
o ROBUSTNESS: Package now explicitly depends on 'utils'.
Version: 0.19.7 [2012-02-22]
BUG FIXES:
o findLargeGaps() did not handle missing values for argument 'chromosome'.
o segmentByCBS(..., knownSegments = knownSegments) would incorrectly throw a
sanity-check exception if 'knownSegments' contains a segment with 'start'
and 'stop' positions being equal.
o Argument 'calls' of plotTracks() for PairedPSCBS was ignored if more than
one chromosome was plotted.
Version: 0.19.6 [2012-01-24]
NEW FEATURES:
o ROBUSTNESS: Now getCallStatistics() for CBS asserts that calls have been
made. If not, an exception is thrown.
Version: 0.19.5 [2012-01-21]
DOCUMENTATION:
o Added details to the help of callLOH() and callAB() on the difference
between (AB,LOH) = (TRUE,FALSE) and (AB,LOH) = (TRUE,NA).
o Corrected some of verbose messages of estimateDeltaLOHByMinC1ForNonAB() for
PairedPSCBS objects.
Version: 0.19.4 [2012-01-10]
CODE REFACTORING:
o Now example(segmentByPairedPSCBS) and the system tests that are run by
'R CMD check' are tuned to (by default) run much faster by segmenting using
fewer data points and bootstrapping using fewer samples. This update was
done to meet the new CRAN policy. By setting environment variable
_R_CHECK_FULL_ to '1' the full data set is used instead.
Version: 0.19.3 [2012-01-09]
NEW FEATURES:
o ROBUSTNESS: Now extractSegments() for PairedPSCBS gives an informative error
message that it is not supported if CNs were segmented using flavor "tcn,dh".
BUG FIXES:
o postsegmentTCN() for PairedPSCBS could generate an invalid 'tcnSegRows'
matrix, where the indices for two consecutive segments would overlap, which
is invalid. Thanks to Minya Pu for reporting on failed sanity check related
to this.
Version: 0.19.2 [2011-12-29]
o ROBUSTNESS: Explicitly added 'digest' to the list of suggested packages.
Version: 0.19.1 [2011-12-13]
NEW FEATURES:
o Added support for callGainsAndLosses(..., method = "ucsf-dmad") of CBS
objects.
Version: 0.19.0 [2011-12-12]
NEW FEATURES:
o Added optional argument 'indices' to getLocusData() to be able to retrieve
the locus-level data as indexed by input data.
BUG FIXES:
o gapsToSegments() gave invalid segments for chromosomes with more than one
gap. Now gapsToSegments() validates argument 'gaps' and asserts that it
returns non-overlapping segments.
DOCUMENTATION:
o Clarified in help("segmentByCBS") how missing values are dealt with.
Version: 0.18.2 [2011-12-07]
NEW FEATURES:
o Now plotTracks() for CBS always returns an invisible object.
BUG FIXES:
o pruneBySdUndo() for CBS did not work with more than one array.
Version: 0.18.1 [2011-12-03]
NEW FEATURES:
o Added drawChangePoints() for AbstractCBS.
o Now pruneByHClust() for AbstractCBS updates the segment means.
o Added writeSegments() for PSCBS object.
o Now print() for AbstractCBS returns getSegments(..., simplify = TRUE).
o Added argument 'simplify' to getSegments().
o Added arguments 'name', 'tags' and 'exts' to writeSegments() and
writeLocusData() and dropped 'filename'.
Version: 0.18.0 [2011-11-28]
NEW FEATURES:
o Added pruneByHClust() for AbstractCBS, with implementation for CBS and
PairedPSCBS.
o extractCNs() for CBS would not return a matrix but a data.frame.
BUG FIXES:
o extractTotalCNs() for CBS would give an error.
Version: 0.17.4 [2011-11-26]
NEW FEATURES:
o Added argument 'updateMeans = TRUE' to callROH() for PairedPSCBS.
o Now bootstrapTCNandDHByRegion() for PairedPSCBS preserves NAs for DH and
(C1,C2) quantiles, if the DH mean level is NA, which can happen when a
segment is called ROH. This also makes sure that a segment called ROH will
not be called AB.
o An internal sanity check of bootstrapTCNandDHByRegion() for PairedPSCBS
would give an error if DH mean levels had been set to NA for segments called
ROH.
Version: 0.17.3 [2011-11-24]
NEW FEATURES:
o Added callSegmentationOutliers() and dropSegmentationOutliers() for data
frames.
o CLEANUP: Renamed field 'position' of the example data to 'x'. This helps us
clean up some of the examples.
BUG FIXES:
o bootstrapTCNandDHByRegion() for PairedPSCBS would give an error, if a
segment did not have any TCN signals, which can occur when known segments
are specified for Paired PSCBS.
Version: 0.17.2 [2011-11-22]
NEW FEATURES:
o Added findLargeGaps() and gapsToSegments().
Version: 0.17.1 [2011-11-21]
BUG FIXES:
o The internal sanity check of testROH() on weights was slightly too
conservative (required to high precision) when it came to asserting that the
sum of the weights equals one.
o resegment() for PairedPSCBS called segmentByCBS() instead of
segmentByPairedPSCBS().
Version: 0.17.0 [2011-11-19]
NEW FEATURES:
o Now it is possible to run Paired PSCBS (without TumorBoost) when only
genotypes but not BAFs are available for the matched normal.
Version: 0.16.3 [2011-11-17]
NEW FEATURES:
o Added resegment() for CBS and PairedPSCBS for easy resegmentation.
o Adjusted segmentByCBS() such that it can handle 'knownSegments' with
chromosome boundaries given as -Inf and +Inf.
o Now argument 'mar' for plotTracks() defaults to NULL.
o ROBUSTNESS: Added redundancy tests for segmentByCBS() and
segmentByPairedPSCBS() with argument 'knownSegments'.
o ROBUSTNESS: Now segmentByCBS() does more validation of 'knownSegments'.
o FIX: extractRegions() for AbstractCBS would also show verbose output.
BUG FIXES:
o Now argument/parameter 'seed' is correctly preserved by segmentByCBS(). So
is 'tbn' for segmentByPairedPSCBS().
o segmentByPairedPSCBS() would give an error when trying to segment DH if the
TCN segment contains no data points, which could happen if 'knownSegments'
specifies an empty segment, e.g. centromere.
o extractSegments() for CBS would throw an error when there were multiple
chromosomes.
Version: 0.16.2 [2011-11-16]
NEW FEATURES:
o Now segmentByCBS(..., w) stores weights 'w', if given, in the locus-level
data table of the returned CBS object.
o Added pruneBySdUndo() for CBS, which does what undo.splits = "sdundo"' for
DNA::segment(), but on the already segmented results.
o Now updateMeans() uses locus-specific weights, iff available.
o Added updateBoundaries() for CBS to update (start,stop) per segment.
o CORRECTNESS: Now updateMeans() for CBS identifies loci via internal
'segRows' field and no longer by locations of segment boundaries, which gave
slightly incorrect estimates for "tied" loci.
Version: 0.16.1 [2011-11-15]
NEW FEATURES:
o Now more segmentation parameters are stored in the CBS object.
o SPEEDUP: Now segmentByCBS() will use memoization to retrieve so called
"sequential boundaries for early stopping", iff any of the
DNAcopy::segment() arguments 'alpha', 'nperm' and 'eta' are specified.
See also DNAcopy::getbdry().
o Added method = "DNAcopy" to estimateStandardDeviation() for CBS, which
estimates the std. dev. using DNAcopy:::trimmed.variance().
BUG FIXES:
o extractSegments() for CBS would throw an error, because in most cases it
would created a corrupt internal 'segRows' field.
Version: 0.16.0 [2011-11-12]
NEW FEATURES:
o Added argument 'oma' and 'mar' to plotTracksManyChromosomes() for
PairedPSCBS for setting graphical parameters when 'add' == FALSE.
o Added callROH().
o Added arguments 'from' and 'adjustFor' to updateMeans().
Version: 0.15.5 [2011-11-04]
BUG FIXES:
o extractSegment() for AbstractCBS would give an error, because it called
itself instead of extractSegments().
Version: 0.15.4 [2011-10-30]
NEW FEATURES:
o Added save() and load() methods to AbstractCBS, which are wrappers for
saveObject() and loadObject() that assert the correct class structure.
Also, the load() method will automatically update the class hierarchy for
CBS and PairedPSCBS objects that were saved before adding class AbstractCBS.
Version: 0.15.3 [2011-10-23]
BUG FIXES:
o callAmplifications() for CBS generated an error, if more than one chromosome
were called.
o The length of a segment must be defined as 'end-start' and not 'end-start+1'
so that the the total length of all segments adds up correctly.
o highlightArmCalls() for CBS did not handle empty chromosomes.
o getCallStatisticsByArms() for CBS threw a error if argument 'genomeData' did
not contain exactly the same chromosomes as in the CBS object.
Version: 0.15.2 [2011-10-21]
NEW FEATURES:
o Added mergeThreeSegments() to AbstractCBS.
BUG FIXES:
o Recent updates caused segmentByPairedPSCBS(data) not to work when 'data' is
a data frame.
Version: 0.15.1 [2011-10-21]
NEW FEATURES:
o By setting 'start' and 'end' to NAs in 'knownSegments' (chromosome must
still be specified), it is possible to insert an empty segment that
disconnects the two flanking segments, e.g. centromere and the two arms.
Version: 0.15.0 [2011-10-20]
NEW FEATURES:
o Added support for specifying priorly known segments, such as chromosome arms
and centromeres, in segmentByCBS() via argument 'knownSegments'.
BUG FIXES:
o CLEANUP: Dropped a stray debug output message in segmentByPairedPSCBS().
Version: 0.14.3 [2011-10-17]
NEW FEATURES:
o Added argument 'asMissing' to dropRegions() for AbstractCBS.
Version: 0.14.2 [2011-10-16]
NEW FEATURES:
o Implemented extractCNs() for CBS and PairedPSCBS.
o Added extractTotalCNs() for CBS.
Version: 0.14.1 [2011-10-14]
NEW FEATURES:
o Added implementation of extractRegions() for AbstractCBS, which utilizes
extractSegments().
o Added abstract extractSegments() and extractSegment() for AbstractCBS.
o Now extractTCNAndDHs() for PairedPSCBS passes '...' to getSegments().
Version: 0.14.0 [2011-10-10]
CODE REFACTORING:
o CLEANUP: Harmonization of several method names.
o CLEANUP: Internal restructuring of the source code files.
Version: 0.13.5 [2011-10-10]
NEW FEATURES:
o Added dropChangePoint() for AbstractCBS, which is just a "name wrapper" for
mergeTwoSegments().
o Added dropRegion() and dropRegions() for AbstractPSCBS, where the former is
a wrapper for the latter dropRegions().
o Added updateMeans() and mergeTwoSegments() for CBS in addition already
available PairedPSCBS versions.
o Relabeled column 'id' to 'sampleName' returned by getSegments().
BUG FIXES:
o For so called "splitter" rows, not all columns returned by getSegments() of
CBS were missing values.
o The object returned by as.CBS() of DNAcopy did not have the correct class
hierarchy.
CODE REFACTORING:
o ROBUSTNESS: Now using getSegments() everywhere possible.
Version: 0.13.4 [2011-10-08]
NEW FEATURES:
o Added all.equal() for AbstractCBS, which does not compare attributes.
o Added optional argument 'regions' to getCallStatistics() of CBS in order to
calculate call statistics on subsets of chromosomes, e.g. chromosome arms.
o Added drawChromosomes() for CBS.
o Added getCallStatisticsByArms(), callArms() and highlightArmCalls() for CBS
objects.
CODE REFACTORING:
o Now internal getChromosomeRanges() of CBS returns a data.frame instead of a
matrix, and first column is now 'chromosome'.
Version: 0.13.3 [2011-10-03]
NEW FEATURES:
o GENERALIZATION: Now segmentByCBS() and segmentByPairedPSCBS() also accepts a
data.frame of locus-level data with column names matching the locus-level
arguments accepted by the corresponding method.
o GENERALIZATION: Now all segmentation result classes (CBS and PSCBS) inherits
from the AbstractCBS class, which provides methods such as getSampleName(),
getChromosomes() and getSegments().
DOCUMENTATION:
o Added lots of more help pages.
CODE REFACTORING:
o CLEANUP: Dropped empty callSegments() for PairedPSCBS.
Version: 0.13.2 [2011-09-30]
NEW FEATURES:
o GENERALIZATION: Now drawLevels() for PairedPSCBS allows for drawing
segmentation results in 'betaT' space.
BUG FIXES:
o plotTracks2(..., panels = "dh") gave an error due to a forgotten assignment.
Version: 0.13.1 [2011-09-06]
NEW FEATURES:
o Added formal class CBS, which holds the segmentation results returned by
segmentByCBS(). Several methods are available for CBS objects, e.g.
nbrOfLoci(), nbrOfSegments(), nbrOfChromosomes(), getChromosomes(),
estimateStandardDeviation() etc.
o Now segmentByCBS() always returns a CBS object. To coerce to a DNAcopy
object (as defined in the DNAcopy class) use as.DNAcopy().
o Added coerce methods as.DNAcopy() for CBS objects and as.CBS() for DNAcopy
objects.
Version: 0.13.0 [2011-09-01]
NEW FEATURES:
o GENERALIZATION: Now segmentByCBS() can process multiple chromosomes.
o Added append() for CBS objects.
BUG FIXES:
o Internal methods plotTracksManyChromosomes() and tileChromosomes() for CBS
did not work at all and therefore neither plotTracks() for CBS with more
than one chromosome.
Version: 0.12.2 [2011-08-27]
CODE REFACTORING:
o CLEANUP: Now R CMD check is no longer giving a note that the package loads
package 'DNAcopy' in .onAttach().
Version: 0.12.1 [2011-08-08]
BUG FIXES:
o If dropSegmentationOutliers() would drop an outlier next to a change point,
such that the total copy-number signal becomes NA, then the sanity checks
that TCN segments always overlaps DH segments would fail. Now the sanity
checks are aware of this special case. These sanity checks were moved from
bootstrapTCNandDHByRegion() to segmentByPairedPSCBS(). Thanks Christine To
at University of Toronto for reporting on this.
Version: 0.12.0 [2011-07-23]
BUG FIXES:
o Recently R devel automatically adds a namespace to a package, if missing.
This caused some of the PSCBS examples to throw an exception related to
incorrect dispatching of cat().
CODE REFACTORING:
o Added a namespace to the package, which will be more or less a requirement
in the next major release of R.
Version: 0.11.7 [2011-07-15]
DOCUMENTATION:
o Added a section to help("segmentByPairedPSCBS") on the importance of doing
a whole-genome PSCBS segmentations if calling AB and LOH states afterward.
o Made it more clear in help("segmentByPairedPSCBS") that arguments 'betaT',
'betaN' and 'muN' may contain NAs for non-polymorphic loci.
Version: 0.11.6 [2011-07-14]
BUG FIXES:
o ROBUSTNESS: In some cases, the segmentation table would contain column names
with incorrect capitalization, e.g. "tcnnbrOfLoci" instead of "tcnNbrOfLoci".
This would cause several downstream methods to give an error. The reason
for this is that the Hmisc package, if loaded after R.utils, overrides
capitalize() in R.utils with another (buggy?) capitalize() function.
To avoid this, we now everywhere specify explicitly that we want the one in
R.utils. Thanks Christine To at University of Toronto for reporting on this.
Version: 0.11.5 [2011-07-10]
BUG FIXES:
o tileChromosomes() for PairedPSCBS was still assuming the old naming
convention of column names. This caused plotTracks() to throw an exception
when plotting multiple chromosomes.
CODE REFACTORING:
o ROBUSTNESS: Fixed partial argument matchings in arrowsC1C2() and
arrowsDeltaC1C2() for PairedPSCBS.
Version: 0.11.4 [2011-07-07]
NEW FEATURES:
o GENERALIZATION: Now the internal estimator function that estimateDeltaLOH()
uses returns -Inf if all segments are called AB, instead of throwing an
exception. This will in turn make callLOH() call all segments to be non-LOH.
DOCUMENTATION:
o Removed obsolete references to the R-forge repository.
BUG FIXES:
o Consecutive calls to callAB(..., force = TRUE) would append additional
'abCall' columns to the segmentation table instead of replacing existing
calls.
Version: 0.11.3 [2011-07-06]
NEW FEATURES:
o ROBUSTNESS: Added a sanity check to estimateDeltaLOHByMinC1AtNonAB() for
PairedPSCBS object. The test asserts that there exist segments that are not
in allelic balance, which are needed in order to estimate DeltaLOH.
DOCUMENTATION:
o The description of argument 'chromosome' for segmentByPairedPSCBS() did not
describe how to segment multiple chromosomes in one call.
Version: 0.11.2 [2011-07-05]
BUG FIXES:
o Output fields 'tcnNbrOfSNPs' and 'tcnNbrOfHets' were mistakenly labeled as
'tcnNbrOr...'. Thanks Christine Ho at UC Berkeley for reporting on this.
Version: 0.11.1 [2011-06-28]
DOCUMENTATION:
o Clarified that argument 'CT' should be tumor copy number ratios relative to
the normal.
o Added Rd help for as.data.frame() of PairedPSCBS.
Version: 0.11.0 [2011-06-14]
SIGNIFICANT CHANGES:
o Renamed all column names of returned data frames such that they follow the
camelCase naming conventions in addition to be somewhat shorter too.
NEW FEATURES:
o GENERALIZATION: Added argument 'columnNamesFlavor' to segmentByCBS().
Version: 0.10.2 [2011-06-07]
CODE REFACTORING:
o CLEANUP: Cleaned up the example():s.
o Added more biocViews categories to DESCRIPTION
Version: 0.10.1 [2011-05-31]
NEW FEATURES:
o GENERALIZATION: The package can now be *installed* without the DNAcopy
package being installed. If package is loaded without DNAcopy installed,
an informative message will explain how to install it.
o Added installDNAcopy(), which will install DNAcopy from Bioconductor.
CODE REFACTORING:
o ROBUSTNESS: Now all DNAcopy functions are called as DNAcopy::nnn().
Version: 0.10.0 [2011-05-29]
SIGNIFICANT CHANGES:
o Renamed package to PSCBS (from 'psCBS').
o Renamed all arguments, variables, and functions referring to 'tau' to refer
to 'delta' reflecting the notation of the Paired PSCBS paper.
o Renamed options, example code and help pages to reflect new package name.
DOCUMENTATION:
o Updated references in help pages.
o Now the paired PSCBS is formally referred to as 'Paired PSCBS'.
Version: 0.9.54 [2011-04-27]
NEW FEATURES:
o Added argument 'maxC' to estimateTauLOHByMinC1ForNonAB().
Version: 0.9.53 [2011-04-14]
o Added argument 'max' to estimateTauAB() and estimateTauLOH().
Version: 0.9.52 [2011-04-14]
BUG FIXES:
o Argument 'minSize' of callAB() and callLOH() had no effect.
Version: 0.9.51 [2011-04-12]
NEW FEATURES:
o Added argument 'minSize' to callAB() and callLOH() for PairedPSCBS.
o Now the a conflicting call in callLOH()/callAB() with argument
xorCalls = TRUE is set to NA to contrast it from a FALSE call.
Version: 0.9.50 [2011-04-12]
NEW FEATURES:
o Added argument 'xorCalls' to callLOH() and callAB() for PairedPSCBS. When
TRUE (the default), a segment that is already called AB will never be called
LOH, and vice versa.
Version: 0.9.49 [2011-04-11]
NEW FEATURES:
o Updated estimateTauABBySmallDH() for PairedPSCBS to use a "symmetric"
quantile estimator.
o Added argument 'midpoint' to estimateTauLOHByMinC1AtNonAB().
BUG FIXES:
o The recent callLOH() would not store the LOH calls.
Version: 0.9.48 [2011-04-10]
NEW FEATURES:
o Added callLOH() for PairedPSCBS, which in turn calls auxiliary methods.
o Added estimateTauLOH() for PairedPSCBS, which in turn calls axillary methods.
o Now callAB(..., force = FALSE) skips the caller if allelic-balance calls
already exist.
DOCUMENTATION:
o Update the example for segmentByPairedPSCBS to reflect the restructured AB
and LOH callers.
Version: 0.9.47 [2011-04-08]
NEW FEATURES:
o Added estimateTauABBySmallDH()
o Added internal weightedQuantile().
DOCUMENTATION:
o Added help pages for more methods.
CODE REFACTORING:
o CLEANUP: Started to restructure the source code files.
Version: 0.9.46 [2011-04-08]
BUG FIXES:
o postsegmentTCN() for PairedPSCBS could generate an invalid 'tcnSegRows'
matrix, where the indices for two consecutive segments would overlap, which
is invalid. This was caught with real data, but it seems to have required a
very rare combination of data in order for it to occur.
Version: 0.9.45 [2011-04-05]
BUG FIXES:
o estimateHighDHQuantileAtAB() for PairedPSCBS would throw an error on an
undefined 'trim' if verbose output was used.
Version: 0.9.44 [2011-02-18]
NEW FEATURES:
o Added estimateHighDHQuantileAtAB() for PairedPSCBS.
Version: 0.9.43 [2011-02-06]
BUG FIXES:
o plotTracks2() queried non-existing argument 'tracks'.
Version: 0.9.42 [2011-02-03]
NEW FEATURES:
o Added estimateKappa() for estimating the normal contamination.
Version: 0.9.41 [2011-02-02]
SIGNFICANT CHANGES:
o Updated default for 'tauAB' of callABandHighAI() and callABandLowC1() to be
estimated from data using estimateTauAB().
NEW FEATURES:
o Added argument 'tauTCN' to estimateTauAB().
Version: 0.9.40 [2011-01-27]
NEW FEATURES:
o Added argument 'flavor' to estimateTauAB() for estimating the AB threshold
using alternative methods.
Version: 0.9.39 [2011-01-19]
NEW FEATURES:
o Added trial version of new plotTracks2(), which will later replace
plotTracks(). Currently it only works for single chromosomes.
o Added support functions, e.g. updateMeans().
Version: 0.9.38 [2011-01-18]
NEW FEATURES:
o Added arguments 'changepoints' and 'col' to plotTracks() for PairedPSCBS.
o Now plotTracks(..., add = FALSE) for PairedPSCBS only sets up subplots if
argument 'tracks' specifies more than one panel.
DOCUMENTATION:
o Documented more plotTracks() arguments for PairedPSCBS.
BUG FIXES:
o Now plotTracks(..., add = TRUE) for PairedPSCBS plots to the current
figure/panel.
Version: 0.9.37 [2011-01-18]
BUG FIXES:
o 'tcnSegRows' and 'dhSegRows' where not updated by extractByRegions() for
PairedPSCBS.
Version: 0.9.36 [2011-01-14]
NEW FEATURES:
o Added estimateTauAB() for estimating the tauAB tuning parameter when calling
segments in allelic balance. Updated example(segmentByPairedPSCBS) to
illustrate how to use it.
o Added extractByRegions() for PairedPSCBS.
Version: 0.9.35 [2011-01-12]
NEW FEATURES:
o Now postsegmentTCN(..., force = TRUE) for PairedPSCBS also updates the TCN
estimates even for segments where the DH segmentation did not find any
additional change points.
Version: 0.9.34 [2010-12-09]
BUG FIXES:
o When there were multiple chromosomes processed by segmentByPairedPSCBS(),
then the returned data object would contain 'betaT' identical to 'betaTN'.
Version: 0.9.33 [2010-12-07]
NEW FEATURES:
o Added callLowC1ByC1() and callABandLowC1().
Version: 0.9.32 [2010-12-03]
BUG FIXES:
o In rare cases the bootstrap sanity checks can indeed produce an invalid
'range', more precisely where (range[,2] >= range[,1]) is not true. This
can happen if there is no variation in the bootstrap estimates. Because of
this we allow for some tolerance.
Version: 0.9.31 [2010-12-02]
NEW FEATURES:
o Added option "psCBS/sanityChecks/tolerance" for specifying the tolerance of
some internal sanity checks.
Version: 0.9.30 [2010-12-01]
CODE REFACTORING:
o Rewrote all code dealing with the identification of loci belong to segments.
The code is now utilizing the 'segRows' element returned by
DNAcopy::segment(). Lots of the code was rewritten and therefore completely
new bugs may have been introduced.
Version: 0.9.25 [2010-11-30]
BUG FIXES:
o Argument 'flavor' of segmentByPairedPSCBS() would be ignored if multiple
chromosomes were segmented.
o extractByChromosome() for PSCBS would call it self instead of
extractByChromosomes().
Version: 0.9.24 [2010-11-28]
BUG FIXES:
o postsegmentTCN() did not handle loci with the same positions and that are
split in two different segments. It also did not exclude loci with missing
values.
Version: 0.9.23 [2010-11-28]
BUG FIXES:
o The algorithm in segmentByCBS() that infers which loci (of the ones share
the same genomic positions) that should be exclude from each segment did not
take missing signals into account.
o Iff argument 'chromosome' to segmentByPairedPSCBS() was of length greater
than one and specified exactly one unique chromosome, then exception
"Number of elements in argument 'chromosome' should be exactly 8712 not
86209 value(s)" would be thrown.
Version: 0.9.22 [2010-11-27]
BUG FIXES:
o bootstrapTCNandDHByRegion() would incorrectly include non-polymorphic loci
in the set of homozygous SNPs during resampling.
o segmentByPairedPSCBS() would not accept missing values in argument
'chromosome'.
Version: 0.9.21 [2010-11-27]
NEW FEATURES:
o Now arguments '...' of segmentByPairedPSCBS() are passed to the two
segmentByCBS() calls.
o Added callSegmentationOutliers(), which can be used to identify single-locus
outliers that have a genomic signal that is clearly outside the expected
range. The dropSegmentationOutliers() sets locus outliers detected by this
method to missing values. This is useful for excluding total copy-number
outliers that otherwise can have a dramatic impact on the non-robust CBS
method.
Version: 0.9.20 [2010-11-26]
NEW FEATURES:
o Added optional argument 'chromosomes' to plotTracks() to plot a subset of
all chromosomes.
o Added extractByChromosomes() for PSCBS.
o Now the default confidence intervals for plotTracks() is (0.05,0.95), if
existing.
o Now all call functions estimate symmetric bootstrap quantiles for
convenience of plotting confidence intervals.
BUG FIXES:
o callABandHighAI() for PairedPSCBS used the old DH-only bootstrap method.
o The statistical sanity checks of the bootstrap estimates would give an error
when only single-sided bootstrap confidence interval was calculated.
o The call functions, for instance callABandHighAI(), would throw 'Error in
quantile.default(x, probs = alpha) : missing values and NaN's not allowed if
'na.rm' is FALSE' unless bootstrapTCNandDHByRegion() was run before.
Version: 0.9.19 [2010-11-23]
NEW FEATURES:
o ROBUSTNESS: Added more sanity checks to bootstrapTCNandDHByRegion().
o WORKAROUND: The precision of the mean levels of DNAcopy::segment() is not
great enough to always compare it to that of R's estimates.
BUG FIXES:
o bootstrapTCNandDHByRegion() would give an error if there was only one
segment.
o segmentByPairedPSCBS() and bootstrapTCNandDHByRegion() would not subset the
correct set of DH signals if there were some missing values in TCN.
Version: 0.9.18 [2010-11-22]
NEW FEATURES:
o Added argument 'calls' to plotTracks() for highlighting called regions.
o Updated callAllelicBalanceByDH() and callExtremeAllelicImbalanceByDH() to
utilize bootstrapTCNandDHByRegion().
o ROBUSTNESS: Now drawConfidenceBands() of PairedPSCBS silently does nothing
if the requested bootstrap quantiles are available.
BUG FIXES:
o bootstrapTCNandDHByRegion() for PairedPSCBS would not correctly detect if
bootstrap results are already available.
Version: 0.9.17 [2010-11-21]
NEW FEATURES:
o Now plotTracks() supports tracks "tcn,c1", "tcn,c2" and "c1,c2" too.
o Added support for flavor "tcn&dh" in segmentByPairedPSCBS(), which contrary
to "tcn,dh" enforces TCN and DH to have the same change points. The default
flavor is now "tcn&dh".
o Added argument 'xlim' to plotTracks() making it possible to zoom in.
Version: 0.9.16 [2010-11-21]
NEW FEATURES:
o Now joinSegments = TRUE is the default for segmentByCBS() and
segmentByPairedPSCBS().
o Added argument 'quantiles' to plotTracks(), which if specified draws
confidence bands previously estimated from bootstrapping.
o Added drawConfidenceBands() for PairedPSCBS.
o Added bootstrapTCNandDHByRegion() for PairedPSCBS.
o Added standalone joinSegments() for CBS results.
o Now segmentByPairedPSCBS() also returns minor and major copy numbers for
each segment.
Version: 0.9.15 [2010-11-21]
NEW FEATURES:
o Adjusted postsegmentTCN() such that the updated TCN segment boundaries are
the maximum of the DH segment and the support by the loci. This means that
postsegmentTCN() will work as expected both when signals where segmented
with 'joinSegments' being TRUE or FALSE.
o Updated plotTracks() for PairedPSCBS such that the TCN segmentation is
colored 'purple' and the DH segmentation 'orange' for TCN and DH only tracks.
Version: 0.9.14 [2010-11-20]
NEW FEATURES:
o Now it is possible to specify the boundaries of the regions to be segmented
as known change points via argument 'knownCPs'.
o Added argument 'joinSegments' to segmentByCBS() and segmentByPairedPSCBS()
in order to specify if neighboring segments should be joined or not.
o Now segmentByCBS() and segmentByPairedPSCBS() allow for unknown genomic
positions as well as missing total CN signals.
Version: 0.9.13 [2010-11-19]
NEW FEATURES:
o Added argument 'joinSegments' to segmentByCBS() in order to specify if
neighboring segments should be joined or not.
Version: 0.9.12 [2010-11-19]
NEW FEATURES:
o Added plotTracks() and drawLevels() etc to CBS results.
o Now segmentByCBS() allows for unknown genomic positions.
o Now segmentByCBS() allows for missing signals.
o Added argument 'preserveOrder' to segmentByCBS(). If TRUE, then the loci in
the returned 'data' object are ordered as the input data, otherwise it is
ordered along the genome.
Version: 0.9.11 [2010-11-16]
NEW FEATURES:
o Now the 'data' object returned by segmentByCBS() contains field 'index' if
and only if the loci had to be reorder along the genome.
DOCUMENTATION:
o Added more details, references to papers, and cross links to other functions
to the help pages.
BUG FIXES:
o In the rare cases where two loci at the same positions are split up into two
neighboring segments, then segmentByPairedPSCBS() would fail to infer which
they were if and only if the loci were not ordered along the genome. This
could happen with for instance Affymetrix GenomeWideSNP_6 data.
Version: 0.9.10 [2010-11-09]
NEW FEATURES:
o Added argument 'cex = 1' to plotTracks().
BUG FIXES:
o It was not possible to plot BAF tracks with plotTracks().
Version: 0.9.9 [2010-11-05]
BUG FIXES:
o segmentByCBS() tried to pass non-existing argument 'undo.split' to
DNAcopy::segment(). It should be 'undo.splits'.
Version: 0.9.8 [2010-11-04]
BUG FIXES:
o There was a stray/debug stop() statement left in segmentByPairedPSCBS()
causing an "error" in the rare case when loci that have the same physical
locations are split into two different segments.
Version: 0.9.7 [2010-11-03]
o ROBUSTNESS: Now bootstrapDHByRegion() uses resample() of R.utils.
BUG FIXES:
o bootstrapDHByRegion() did not sample from the correct unit(s) when there was
only one DH signal.
Version: 0.9.6 [2010-11-02]
NEW FEATURES:
o Added arguments 'undoTCN' and 'undoDH' to segmentByPairedPSCBS().
o Added argument 'undo' to segmentByCBS(), which corresponds to
undo.splits = "sdundo" and undo.SD = undo, if undo < +Inf.
BUG FIXES:
o Arguments 'alphaTCN' and 'alphaDH' of segmentByPairedPSCBS() were not used
when more than one chromosome were segmented.
Version: 0.9.5 [2010-11-01]
NEW FEATURES:
o Added arguments 'alphaAB' and 'alphaHighAI' to callABandHighAI().
BUG FIXES:
o bootstrapDHByRegion() would give an error if only a single quantile was
requested.
o bootstrapDHByRegion() would give "Error in if (nbrOfUnits > segJJ[,
"dh.num.mark"]) { : missing value where TRUE/FALSE needed" when
'dh.num.mark' was NA.
Version: 0.9.4 [2010-10-25]
NEW FEATURES:
o Now the default is a 95% confidence interval for calls.
o Now segmentByCBS() also returns element 'lociNotPartOfSegment', if there are
segments that share end points, which can happen if a change point is called
in middle of a set of loci that have the same genomic positions. In such
cases, 'lociNotPartOfSegment' specifies which loci are *not* part of which
segment. Then by identifying the loci that are within a segment by their
positions and excluding any of the above, one knows exactly which loci CBS
included in each segment.
BUG FIXES:
o Now bootstrapDHByRegion() for PairedPSCBS handles the rare case when markers
with the same positions are split in two different segments.
o Now the correct set of loci are extracted from each TCN segment, in the rare
case that two neighboring TCN segments have the same end points.
Version: 0.9.3 [2010-10-25]
NEW FEATURES:
o Added argument 'ciRange' to callAllelicBalance() and
callExtremeAllelicImbalance().
BUG FIXES:
o bootstrapDHByRegion() for PairedPSCBS would bootstrap from the incorrect set
of loci when the DH region contained only one locus.
o bootstrapDHByRegion() for PairedPSCBS would bootstrap from the incorrect set
of loci if more than one chromosome was available.
Version: 0.9.2 [2010-10-24]
BUG FIXES:
o plotTracks() would give "Error: object 'nbrOfLoci' not found' for
whole-genome plots.
Version: 0.9.1 [2010-10-20]
NEW FEATURES:
o Now plotTracks() can plot whole-genome data.
Version: 0.9.0 [2010-10-18]
NEW FEATURES:
o Added arguments 'alphaTCN' and 'alphaDH' to segmentByPairedPSCBS() with
defaults according to the paper.
Version: 0.8.3 [2010-10-18]
NEW FEATURES:
o Now segmentByPairedPSCBS() can segment multiple chromosomes.
Version: 0.8.2 [2010-10-17]
NEW FEATURES:
o Added argument 'tbn' to segmentByPairedPSCBS() specifying whether
TumorBoostNormalization should be applied or not.
Version: 0.8.1 [2010-10-10]
SIGNIFICANT CHANGES:
o The default for segmentByPairedPSCBS() is now to segment TCN on the original
scale, not the sqrt().
NEW FEATURES:
o Added plotTracks() for PairedPSCBS.
Version: 0.8.0 [2010-10-06]
CODE REFACTORING:
o CLEAN UP: Removed all old code, native code and help pages.
Version: 0.7.8 [2010-10-03]
NEW FEATURES:
o Added optional argument 'chromosome' to segmentByCBS(). Note that at this
point it is only used for annotating the results; it can not be used to
segmented multiple chromosomes at ones.
Version: 0.7.7 [2010-09-26]
NEW FEATURES:
o Now subsetBySegments() and postsegmentTCN() for PairedPSCBS handles multiple
chromosomes.
Version: 0.7.6 [2010-09-24]
NEW FEATURES:
o Added support to annotating and subsetting also by chromosomes, as well as
appending segmentation results from different chromosomes together.
Version: 0.7.5 [2010-09-21]
NEW FEATURES:
o Added postsegmentTCN() for PairedPSCBS, which updates the TCN segment start
and ends, estimates and counts given the DH segments.
Version: 0.7.4 [2010-09-18]
NEW FEATURES:
o Added argument 'chromosome' to segmentByPairedPSCBS(), which, if given, adds
a chromosome column to the data and segmentation results.
BUG FIXES:
o plot() for PairedPSCBS used a non-defined variable.
Version: 0.7.3 [2010-09-16]
NEW FEATURES:
o Added callABandHighAI() for calling paired PSCBS segmentation results.
CODE REFACTORING:
o Added internal bootstrapping functions.
Version: 0.7.2 [2010-09-15]
NEW FEATURES:
o Added more methods for the PSCBS class.
Version: 0.7.1 [2010-09-08]
NEW FEATURES:
o Added more methods for the PSCBS class.
o Now segmentByPairedPSCBS() also returns the TumorBoost normalized data.
Version: 0.7.0 [2010-09-04]
NEW FEATURES:
o Updated segmentByPairedPSCBS() to provide two-step segmentation from first
segmenting the total copy numbers and then the decrease-of-heterozygosity
signals. Added utility functions for plotting the results. The code for
calling allelic imbalance and LOH is still to be added.
Version: 0.6.3 [2010-09-02]
NEW FEATURES:
o Now segmentByCBS() also works if there are no data points.
Version: 0.6.2 [2010-07-14]
NEW FEATURES:
o Added callNaiveHeterzygotes() which is a cleaned up version of
findheterozygous(). Added Rd example that asserts that the two are identical
and compares the calls to those of aroma.light::callNaiveGenotypes().
Version: 0.6.1 [2010-07-09]
NEW FEATURES:
o Added low-level segmentByPairedPSCBS(), which runs paired PSCBS segmentation
on a single sample and a single chromosome. It only segments; it does not
call segments. This is only a stub in the sense that it still does not
adjust p-values etc.
o Added low-level segmentByCBS(), which runs CBS segmentation on a single
sample and a single chromosome.
o BACKWARD COMPATIBILITY: Now psCNA() returns a list of length 8.
o Reverted psSegment() back to v0.5.6.
Version: 0.6.0 [2010-07-08]
NEW FEATURES:
o Now psSegmentPaired() returns a data frame (no longer a matrix).
o CLEANUP: Created psSegmentPaired() from psSegment().
CODE REFACTORING:
o CLEANUP: Major cleanup, i.e. renaming variables, reordering etc.
o ROBUSTNESS: Replaced all 1:n with seq(length = n) to deal with n == 0.
o ROBUSTNESS: Now all list elements are referenced by name.
o ROBUSTNESS: Now all iterator variables are written as ii, jj etc.
o Using setMethodS3() of R.methodsS3 to define S3 method.
o Dropping NAMESPACE while package is finished. This makes it easier to patch
methods etc.
Version: 0.5.6 [2010-07-07]
DOCUMENTATION:
o Added example(psSegment).
BUG FIXES:
o Previous clean up introduced bugs.
o The dynamic library for hrmode() was not loaded.
Version: 0.5.5 [2010-05-05]
CODE REFACTORING:
o CLEAN UP/ROBUSTNESS: Major code clean up.
Version: 0.5.4 [2010-04-30]
CODE REFACTORING:
o Added internal hrmode().
o CLEANUP: Renamed source files to match function names. Only only function
per source file.
Version: 0.5.3 [2010-04-22]
SIGNIFICANT CHANGES:
o ABO updated the psCBS algorithm.
Version: 0.5.2 [2010-0?-??]
o ???
Version: 0.5.1 [2010-03-31]
SIGNIFICANT CHANGES:
o Now psSegment(..., matching.reference = TRUE) does TumorBoost normalization
on the allele B fractions before segmentation.
Version: 0.5.0 [2010-03-12]
o Added to R-forge repository.
|