Estimate Pairwise Interactions from multidimensional features


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Documentation for package ‘RNAinteract’ version 1.8.0

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RNAinteract-package Analysis of Pairwise Interaction Screens.
bindscreens bind RNAinteract objects along screens
computePI compute pairwise interaction
computePValues compute p-values
createCellHTSFromFiles create cellHTS2 object from text files
createRNAinteract create a RNAinteract object
createRNAinteractFromFiles create an RNAinteract object from text files
doublePerturbationGrob Double Perturbation Plot Grob
embedPCA Computes a PCA for a pairwise interaction matrix.
endReport start and end a RNAinteract report
estimateMainEffect estimate main effect
getChannelNames get names of screens and channels
getData Primary access function for all screen data.
getIndDesignData Extract replicates measurements from the screen.
getMain get main effects
getMainNeg get main effects
getReplicateData Extract replicates measurements from the screen.
getScale get scale information for a channel.
getScreenNames get names of screens and channels
grid.doublePerturbation Double Perturbation Plot Grob
grid.sgiHeatmap A heatmap grob
normalizeMainEffectQuery normalize query main effect
normalizeMainEffectTemplate normalize template main effect
normalizePlateEffect Normalization of plate effects
plotDoublePerturbation Double Perturbation Plot
plotHeatmap plots a heatmap for an interaction screen.
postDrawDetails.doublePerturbation Double Perturbation Plot Grob
reportAnnotation Specialized report functions
reportDoublePerturbation Specialized report functions
reportGeneLists Specialized report functions
reportHeatmap Specialized report functions
reportMainEffects Specialized report functions
reportNetworks Specialized report functions
reportScreenData Specialized report functions
reportStatistics Specialized report functions
RNAinteract Analysis of Pairwise Interaction Screens.
RNAinteract-class Class "RNAinteract"
sgi Dataset of class 'RNAinteract'
sgisubset subset of an RNAinteract object.
sgisubsetQueryDesign Subsetting query genes in a RNAinteract object.
show-method Class "RNAinteract"
startReport start and end a RNAinteract report
summarizeScreens summarize screens
swaptree Swaps a branch of a hclust object.