Statistical analysis of high-throughput RNAi screens


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Documentation for package ‘RNAither’ version 2.24.0

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RNAither-package Statistical analysis of high-throughput RNAi screens
BScore BScore normalization
channelPlot Plot signal channels against each other
closestToZero Return the replicate value closest to zero
compareHits Searching for common hits between different scoring methods
compareReplicaPlates Compare replica plates
compareReplicates Compare replicate values
compareReplicateSD Plot the standard deviation of replicates
compareReplicateSDPerScreen Plot the standard deviation of replicates for each experiment
controlDensity Plotting the control density
controlDensityPerPlate Plotting the control density per plate
controlDensityPerScreen Plotting the control density per experiment
controlNorm Normalization on controls
createSubset Creating a subset of a dataset according to a certain column value
dataset a typical example RNAi dataset
datasetDrosophila Genome-wide RNAi screen of cell viability in Drosophila Kc167 cells by Boutros et al.
discardLabtek Remove a complete plate from the analysis
discardWells Remove wells from the analysis
divideChannels Divide channel values
divNorm Mean, median, ... , normalization
DRQualControl Computing the dynamic range
eraseDataSetColumn Remove columns from dataset
findReplicates Find all replicates of a certain siRNA/gene in a dataset
furthestFromZero Return the replicate value furthest from zero
generateDatasetFile Generate Dataset File
generateReplicateMat Generate a matrix of replicates
generateRepMatNoFilter Generate a matrix of replicates (II)
gseaAnalysis Perform a GSEA analysis of a list of genes
header a typical header of an example RNAi dataset
headerDrosophila the header of the genome-wide RNAi screen of cell viability in Drosophila Kc167 cells by Boutros et al.
hitselectionPval Selecting hits according to p-values
hitselectionZscore Selecting hits according to ZScores
hitselectionZscorePval Selecting hits according to ZScores and p-values
incorporatepValVec Incorporate a vector of p-values into a dataset
indexSubset Saving the indexes of a subset in the main dataset
joinDatasetFiles Join dataset files
joinDatasets Join datasets
LiWongRank Li Wong rank / invariant probeset normalization
lowessNorm Lowess normalization
mainAnalysis Wrapper function for full automated analysis
makeBoxplot4PlateType Generate a boxplot of the data per plate
makeBoxplotControls Generate a boxplot of the data vs. the controls
makeBoxplotControlsPerPlate Generate a boxplot of the data vs. the controls for each plate
makeBoxplotControlsPerScreen Generate a boxplot of the data vs. the controls for each experiment
makeBoxplotPerPlate Generate a boxplot of the data per plate
makeBoxplotPerScreen Generate a boxplot of the data per experiment
MannWhitney Perform a Mann-Whitney test
multTestAdjust Adjust p-values for multiple testing
numCellQualControl Quality control of the number of cells
orderGeneIDs Order a dataset
percCellQualControl Quality control of the percentage of cells
plotBar Plot signal intensities per well
plotControlHisto Plot a histogram of the data values and controls
plotControlHistoPerplate Plot a histogram of the data values and controls per plate
plotControlHistoPerscreen Plot a histogram of the data values and controls per experiment
plotHisto Plot a histogram of the data values
plotHistoPerplate Plot a histogram of the data values per plate
plotHistoPerscreen Plot a histogram of the data values per experiment
plotQQ Make a QQ plot
plotQQperplate Make a QQ plot per plate
plotQQperscreen Make a QQ plot per experiment
pValVec1 A vector of p-values after a median normalization and a t-test
pValVec2 A vector of p-values after a Mann-Whitney test
quantileNormalization Quantile normalization
RankProduct Perform a Rank Product test
replicatesCV Compute the correlation of variation (CV)
replicatesSpearmancor Compute the correlation coefficient betwenn replicates or experiments
rms Compute the replicate root mean square
RNAither Statistical analysis of high-throughput RNAi screens
rnaither Wrapper function for full automated analysis
saveDataset Save the normalized dataset into a dataset text file
saveOldIntensityColumns Save old intensity value columns
savepValVec Save p-values to file
scoredDataset1 A dataset containing an additional column showing the p-values, after a median normalization and a t-test
scoredDataset2 A dataset containing an additional column showing the p-values after a Mann-Whitney test
SNRQualControl Computing the SNR
spatialDistrib Generate spatial plots of intensity values
spatialDistribHits Plotting the spatial distribution of the hits
subtractBackground Background substraction
sumChannels Summarize channels
summarizeReps Generate a new dataset with summarized replicates
summarizeRepsNoFiltering Generate a new dataset with summarized replicates
trim Compute the replicate mean with trimmed values
Ttest Perform a Student's t-test
varAdjust Variance adjustment
vennDiag Plotting a Venn Diagram to compare hits
volcanoPlot Making a volcano plot
ZPRIMEQualControl Computing the Z' factor
ZScore ZScore normalization
ZScorePerScreen ZScore normalization per experiment
ZScorePlot Plot normalized intensity values per well
ZScorePlotTwo Plot signal intensities per well (II)