Man pages for Bioconductor-mirror/RNAither
Statistical analysis of high-throughput RNAi screens

BScoreBScore normalization
channelPlotPlot signal channels against each other
closestToZeroReturn the replicate value closest to zero
compareHitsSearching for common hits between different scoring methods
compareReplicaPlatesCompare replica plates
compareReplicatesCompare replicate values
compareReplicateSDPlot the standard deviation of replicates
compareReplicateSDPerScreenPlot the standard deviation of replicates for each experiment
controlDensityPlotting the control density
controlDensityPerPlatePlotting the control density per plate
controlDensityPerScreenPlotting the control density per experiment
controlNormNormalization on controls
createSubsetCreating a subset of a dataset according to a certain column...
dataseta typical example RNAi dataset
datasetDrosophilaGenome-wide RNAi screen of cell viability in Drosophila Kc167...
discardLabtekRemove a complete plate from the analysis
discardWellsRemove wells from the analysis
divideChannelsDivide channel values
divNormMean, median, ... , normalization
DRQualControlComputing the dynamic range
eraseDataSetColumnRemove columns from dataset
findReplicatesFind all replicates of a certain siRNA/gene in a dataset
furthestFromZeroReturn the replicate value furthest from zero
generateDatasetFileGenerate Dataset File
generateReplicateMatGenerate a matrix of replicates
generateRepMatNoFilterGenerate a matrix of replicates (II)
gseaAnalysisPerform a GSEA analysis of a list of genes
headera typical header of an example RNAi dataset
headerDrosophilathe header of the genome-wide RNAi screen of cell viability...
hitselectionPvalSelecting hits according to p-values
hitselectionZscoreSelecting hits according to ZScores
hitselectionZscorePvalSelecting hits according to ZScores and p-values
incorporatepValVecIncorporate a vector of p-values into a dataset
indexSubsetSaving the indexes of a subset in the main dataset
joinDatasetFilesJoin dataset files
joinDatasetsJoin datasets
LiWongRankLi Wong rank / invariant probeset normalization
lowessNormLowess normalization
mainAnalysisWrapper function for full automated analysis
makeBoxplot4PlateTypeGenerate a boxplot of the data per plate
makeBoxplotControlsGenerate a boxplot of the data vs. the controls
makeBoxplotControlsPerPlateGenerate a boxplot of the data vs. the controls for each...
makeBoxplotControlsPerScreenGenerate a boxplot of the data vs. the controls for each...
makeBoxplotPerPlateGenerate a boxplot of the data per plate
makeBoxplotPerScreenGenerate a boxplot of the data per experiment
MannWhitneyPerform a Mann-Whitney test
multTestAdjustAdjust p-values for multiple testing
numCellQualControlQuality control of the number of cells
orderGeneIDsOrder a dataset
percCellQualControlQuality control of the percentage of cells
plotBarPlot signal intensities per well
plotControlHistoPlot a histogram of the data values and controls
plotControlHistoPerplatePlot a histogram of the data values and controls per plate
plotControlHistoPerscreenPlot a histogram of the data values and controls per...
plotHistoPlot a histogram of the data values
plotHistoPerplatePlot a histogram of the data values per plate
plotHistoPerscreenPlot a histogram of the data values per experiment
plotQQMake a QQ plot
plotQQperplateMake a QQ plot per plate
plotQQperscreenMake a QQ plot per experiment
pValVec1A vector of p-values after a median normalization and a...
pValVec2A vector of p-values after a Mann-Whitney test
quantileNormalizationQuantile normalization
RankProductPerform a Rank Product test
replicatesCVCompute the correlation of variation (CV)
replicatesSpearmancorCompute the correlation coefficient betwenn replicates or...
rmsCompute the replicate root mean square
rnaitherWrapper function for full automated analysis
RNAither-packageStatistical analysis of high-throughput RNAi screens
saveDatasetSave the normalized dataset into a dataset text file
saveOldIntensityColumnsSave old intensity value columns
savepValVecSave p-values to file
scoredDataset1A dataset containing an additional column showing the...
scoredDataset2A dataset containing an additional column showing the...
SNRQualControlComputing the SNR
spatialDistribGenerate spatial plots of intensity values
spatialDistribHitsPlotting the spatial distribution of the hits
subtractBackgroundBackground substraction
sumChannelsSummarize channels
summarizeRepsGenerate a new dataset with summarized replicates
summarizeRepsNoFilteringGenerate a new dataset with summarized replicates
trimCompute the replicate mean with trimmed values
TtestPerform a Student's t-test
varAdjustVariance adjustment
vennDiagPlotting a Venn Diagram to compare hits
volcanoPlotMaking a volcano plot
ZPRIMEQualControlComputing the Z' factor
ZScoreZScore normalization
ZScorePerScreenZScore normalization per experiment
ZScorePlotPlot normalized intensity values per well
ZScorePlotTwoPlot signal intensities per well (II)
Bioconductor-mirror/RNAither documentation built on May 31, 2017, 11:36 p.m.