/usr/lib/R/site-library/rtracklayer/NAMESPACE is in r-bioc-rtracklayer 1.24.2-1.
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 | useDynLib(rtracklayer, .registration = TRUE)
## ============================================================
## Import
## ============================================================
import(methods)
import(BiocGenerics)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### base packages
###
importFrom("stats", offset, setNames)
importFrom("utils", count.fields, URLdecode, URLencode, browseURL, download.file,
read.table, type.convert, write.table)
importFrom("tools", file_path_as_absolute, file_path_sans_ext)
importFrom("grDevices", col2rgb, rgb)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Non-bioconductor packages
###
importFrom("XML", getNodeSet, xmlValue, xmlAttrs, htmlTreeParse,
xmlInternalTreeParse, parseURI, newXMLNode, xmlChildren,
addChildren, removeChildren)
importMethodsFrom("XML", saveXML)
importFrom("RCurl", curlUnescape, fileUpload, getCurlHandle, getForm, getURL,
postForm)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Bioconductor packages
###
import(XVector)
importClassesFrom("IRanges",
IRanges, RangedData, RangedDataList,
Vector, DataTableORNULL, characterORNULL,
RangedSelection, SimpleList, DataFrame, RangesList,
Rle, RleList)
importFrom("IRanges", CharacterList, DataFrame, IRanges, RangedDataList,
RangedData, RangesList, RangedSelection, RleList, isSingleString,
recycleIntegerArg, isSingleStringOrNA,
isTRUEorFALSE, isSingleNumberOrNA, PartitioningByWidth,
PartitioningByEnd, mseqapply)
importMethodsFrom("IRanges", elementLengths, window,
start, end, width, range,
"start<-", "end<-", "width<-",
split, lapply, sapply, unlist, unique,
as.vector, as.list, as.data.frame, as.factor,
colnames, rownames,
"colnames<-","rownames<-",
ranges, values, score,
"ranges<-", "values<-", "score<-",
space, universe, metadata,
"universe<-", "metadata<-",
isDisjoint, queryHits, findOverlaps, reduce, nrow, summary,
resize, mcols, "mcols<-", togroup, Rle, "active<-", collapse,
coverage, findOverlaps, reflect, relist, runValue, shift,
subjectHits, subsetByOverlaps, tile, togroup)
importClassesFrom("GenomicRanges", GenomicRanges, GRanges, GRangesList,
GenomicRangesList, Seqinfo, GIntervalTree,
SimpleGenomicRangesList)
importFrom("GenomicRanges", GRanges, GRangesList, Seqinfo)
importMethodsFrom("GenomicRanges", seqnames, seqlengths, strand, "strand<-",
seqinfo, "seqinfo<-", seqlevels, "seqlevels<-", "seqnames<-",
genome, "genome<-", merge)
importFrom("Biostrings", get_seqtype_conversion_lookup, writeXStringSet,
DNAStringSet)
importMethodsFrom("Biostrings", masks, "masks<-", getSeq)
importClassesFrom("Biostrings", DNAStringSet, XStringSet)
importFrom("BSgenome", installed.genomes, bsapply)
importMethodsFrom("BSgenome", releaseDate, organism,
providerVersion, provider)
importClassesFrom("BSgenome", BSgenome)
importFrom("Rsamtools", indexTabix, bgzip, TabixFile, index)
importMethodsFrom("Rsamtools", ScanBamParam, asBam, headerTabix, isOpen, path,
scanTabix)
importClassesFrom("Rsamtools", RsamtoolsFile, TabixFile, BamFile)
importMethodsFrom("GenomicAlignments", readGAlignmentsFromBam, cigar)
importClassesFrom("GenomicAlignments", GAlignments)
## ============================================================
## Export
## ============================================================
exportClasses(BrowserSession, BrowserView, BrowserViewList,
UCSCSession, UCSCView,
UCSCData, TrackLine, BasicTrackLine, GraphTrackLine,
Bed15TrackLine, UCSCTrackModes, BigWigSelection,
UCSCSchema, Quickload, QuickloadGenome)
## File classes
exportClasses(RTLFile, CompressedFile, GFFFile, UCSCFile, BEDFile, WIGFile,
ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile,
BED15File, GTFFile, GVFFile, BigWigFile, BigWigFileList,
TwoBitFile)
exportMethods(activeView, "activeView<-", blocks, browseGenome,
browserSession, "browserSession<-",
browserView, browserViews,
close, export, export.bed, export.bed15,
export.bedGraph, export.gff, export.gff1, export.gff2,
export.gff3, export.ucsc, export.wig, export.bw,
export.2bit,
import, import.bed, import.bed15, import.bedGraph,
import.gff, import.gff1, import.gff2, import.gff3,
import.ucsc, import.wig, import.bw, import.chain, import.2bit,
"sequence<-", "track<-",
track, trackNames, "trackNames<-", getTable,
tableNames, trackName, "trackName<-",
tableName, "tableName<-",
ucscTrackModes, "ucscTrackModes<-",
ucscSchema,
coerce, initialize,
show, summary, "[", ucscTableQuery,
genome, "genome<-", chrom, "chrom<-", range, "range<-",
visible, "visible<-",
liftOver, offset, reversed,
nrow, formatDescription,
referenceSequence, "referenceSequence<-",
asBED, asGFF,
split,
## from IRanges
start, end, "start<-", "end<-",
score, "score<-",
as.data.frame, space, mcols,
## from GenomicRanges
strand, seqinfo, "seqinfo<-",
## from BSgenome
organism, releaseDate, getSeq
)
export(genomeBrowsers, start, end, strand, "start<-", "end<-", width, "width<-",
ranges, values, GenomicData, GenomicSelection,
score, "score<-", as.data.frame, space,
ucscGenomes, BigWigSelection, GRangesForUCSCGenome,
GRangesForBSGenome, summary, seqinfo, genome, "genome<-",
uri, Quickload, quickload, QuickloadGenome,
organism, releaseDate, mcols, wigToBigWig,
SeqinfoForBSGenome, SeqinfoForUCSCGenome, resource, path,
FileForFormat)
export(GFFFile, UCSCFile, BEDFile, WIGFile,
ChainFile, FastaFile, GFF1File, GFF2File, GFF3File, BEDGraphFile,
BED15File, GTFFile, GVFFile, BigWigFile, BigWigFileList, TwoBitFile)
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