# Statistical analysis of high-throughput RNAi screens

## Documentation for package ‘RNAither’ version 2.2.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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)