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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 | 01.Introduction Introduction to the LIMMA Package
02.Classes Classes Defined by this Package
03.ReadingData Reading Microarray Data from Files
04.Background Background Correction
05.Normalization Normalization of Microarray Data
06.LinearModels Linear Models for Microarrays
07.SingleChannel Individual Channel Analysis of Two-Color
Microarrays
08.Tests Hypothesis Testing for Linear Models
09.Diagnostics Diagnostics and Quality Assessment
10.Other Other Functions
EList-class Expression List - class
FStat Multiple Testing Genewise Across Contrasts
LargeDataObject-class Large Data Object - class
MAList-class M-value, A-value Expression List - class
MArrayLM-class Microarray Linear Model Fit - class
PrintLayout-class Print Layout - class
QualityWeights Spot Quality Weights
RGList-class Red, Green Intensity List - class
TestResults-class Matrix of Test Results - class
alias2Symbol Convert Gene Alias to Official Gene Symbols
anova.MAList ANOVA Table - method
arrayWeights Array Quality Weights
arrayWeightsQuick Array Quality Weights
as.MAList Convert marrayNorm Object to an MAList Object
as.data.frame.MAList Turn a Microarray Linear Model Object into a
Dataframe
as.matrix.RGList Turn a Microarray Data Object into a Matrix
asMatrixWeights asMatrixWeights
auROC Area Under Receiver Operating Curve
avearrays Average Over Replicate Arrays
avedups Average Over Duplicate Spots
avereps Average Over Irregular Replicate Probes
backgroundCorrect Correct Intensities for Background
blockDiag Block Diagonal Matrix
bwss Between and within sums of squares
bwss.matrix Between and within sums of squares for matrix
cbind Combine RGList, MAList, EList or EListRaw
Objects
changeLog Limma Change Log
contrasts.fit Compute Contrasts from Linear Model Fit
controlStatus Set Status of each Spot from List of Spot Types
convest Estimate Proportion of True Null Hypotheses
decideTests Multiple Testing Across Genes and Contrasts
designI2M Convert Individual Channel Design Matrix to M-A
Format
dim.RGList Retrieve the Dimensions of an RGList, MAList or
MArrayLM Object
dimnames.RGList Retrieve the Dimension Names of an RGList,
MAList, EList, EListRaw or MArrayLM Object
duplicateCorrelation Correlation Between Duplicates
ebayes Empirical Bayes Statistics for Differential
Expression
exprs.MA Extract Log-Expression Matrix from MAList
fitFDist Moment Estimation of Scaled F-Distribution
fitted.MArrayLM Fitted Values Method for MArrayLM Fits
genas Genuine Association of Gene Expression Profiles
geneSetTest Mean-rank Gene Set Test
getEAWP Extract Basic Data from Microarray Data Objects
getLayout Extract the Print Layout of an Array from the
GAL File
getSpacing Get Numerical Spacing
gls.series Fit Linear Model to Microarray Data by
Generalized Least Squares
gridr Row and Column Positions on Microarray
heatdiagram Stemmed Heat Diagram
helpMethods Prompt for Method Help Topics
imageplot Image Plot of Microarray Statistics
imageplot3by2 Write Imageplots to Files
intraspotCorrelation Intra-Spot Correlation for Two Color Data
is.fullrank Check for Full Column Rank
isNumeric Test for Numeric Argument
kooperberg Kooperberg Model-Based Background Correction
for GenePix data
limmaUsersGuide View Limma User's Guide
lm.series Fit Linear Model to Microrray Data by Ordinary
Least Squares
lmFit Linear Model for Series of Arrays
lmscFit Fit Linear Model to Individual Channels of
Two-Color Data
loessFit Fast Simple Loess
ma3x3.matrix Two dimensional Moving Averages with 3x3 Window
makeContrasts Construct Matrix of Custom Contrasts
makeUnique Make Values of Character Vector Unique
mdplot mdplot
merge.RGList Merge RGList or MAList Data Objects
mergeScans Merge two scans of two-color arrays
modelMatrix Construct Design Matrix
modifyWeights modifyWeights
mrlm Fit Linear Model to Microrray Data by Robust
Regression
nec NormExp Background Correction and Normalization
Using Control Probes
normalizeBetweenArrays
Normalize Between Arrays
normalizeCyclicLoess Normalize Columns of a Matrix by Cyclic Loess
normalizeForPrintorder
Print-Order Normalization
normalizeMedianAbsValues
Normalize Columns of a Matrix to have the
Median Absolute Value
normalizeQuantiles Normalize Columns of a Matrix to have the same
Quantiles
normalizeRobustSpline Normalize Single Microarray Using Shrunk Robust
Splines
normalizeVSN Variance Stabilizing Normalization (vsn)
normalizeWithinArrays Normalize Within Arrays
normexp.fit Fit Normal+Exp Convolution Model to Observed
Intensities
normexp.fit.control Normexp Model Parameter Estimation Aided by
Negative Controls
normexp.fit.detection.p
Estimate Normexp Model Parameter Using Negative
Controls Inferred from Regular Probes
normexp.signal Expected Signal Given Observed Foreground Under
Normal+Exp Model
plotDensities Individual-channel Densities Plot
plotFB FB-Plot
plotMA MA-Plot
plotMA3by2 Write MA-Plots to Files
plotMDS Multidimensional scaling plot of microarray
data
plotPrintTipLoess MA Plots by Print-Tip Group
plotRLDF Plot of regularized linear discriminant
functions for microarray data
plotSA Sigma vs A plot for microarray linear model
plotlines plotlines
poolVar Pool Sample Variances with Unequal Variances
printHead Print Leading Rows of Large Objects
printorder Identify Order in which Spots were Printed
printtipWeights Sub-array Quality Weights
propexpr Estimate Proportion of Expressed Probes
protectMetachar Protect Metacharacters
qqt Student's t Quantile-Quantile Plot
read.columns Read specified columns from a file
read.ilmn Read Illumina Expression Data
read.ilmn.targets Read Illumina Data from a Target Dataframe
read.maimages Read RGList or EListRaw from Image Analysis
Output Files
readGAL Read a GAL file
readGenericHeader Read Header Information from Image Analysis Raw
Data File
readImaGeneHeader Read ImaGene Header Information
readSpotTypes Read Spot Types File
readTargets Read Targets File
removeBatchEffect Remove Batch Effect
removeExt Remove Common Extension from File Names
residuals.MArrayLM Extract Residuals from MArrayLM Fit
roast Rotation Gene Set Tests
romer Rotation Gene Set Enrichment Analysis
selectModel Select Appropriate Linear Model
squeezeVar Squeeze Sample Variances
strsplit2 Split Composite Names
subsetting Subset RGList, MAList, EList or MArrayLM
Objects
summary.RGList Summaries of Microarray Data Objects
symbols2indices Convert Gene Set Symbols to Indices
targetsA2C Convert Two-Color Targets Dataframe from
One-Row-Per-Array to One-Row-Per-Channel
tmixture.vector Estimate Scale Factor in Mixture of
t-Distributions
topRomer Top Gene Set Testing Results from Romer
toptable Table of Top Genes from Linear Model Fit
trigammaInverse Inverse Trigamma Function
trimWhiteSpace Trim Leading and Trailing White Space
uniquegenelist Eliminate Duplicate Names from the Gene List
unwrapdups Unwrap Duplicate Spot Values from Rows into
Columns
vennCounts Venn Diagrams
volcanoplot Volcano Plot
voom Transform RNA-Seq Data Ready for Linear
Modelling
weighted.median Weighted Median
write.fit Write MArrayLM Object to a File
zscoreGamma Z-score Equivalents
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