Package index • splitTypeR

All functions

ListOrNULL-class: Class Union for list or NULL
MatrixOrNULL-class: Class Union for matrix or NULL
SplitTypeRdata-class: An S4 class to represent the splitTypeR data
SplitTypeRdata(): Create a SplitTypeRdata object
classification(<SplitTypeRdata>): Getter for the classification slot in a SplitTypeRdata class
`classification<-`(<SplitTypeRdata>): Replacement of the classification slot in a SplitTypeRdata object
`classification<-`(): Generic function for replacement of the classification slot in a class
classification(): Generic function for getting the classification slot in a class
expNormalCountsDemo: Simulated normalized expected counts for 30 demonstration samples
getGeneSignatures(): Return the selected gene list signatures
getGeneSignaturesNames(): List the names of the available signatures
getGenesInSignature(): Return the genes for a specific signature
gsvaResults(<SplitTypeRdata>): Getter for the signatures slot in a SplitTypeRdata class
`gsvaResults<-`(<SplitTypeRdata>): Replacement of gsvaResults slot in a SplitTypeRdata object
`gsvaResults<-`(): Generic function for replacement of gsvaResults slot in a class
gsvaResults(): Generic function for getting the gsvaResults slot in a class
model(<SplitTypeRdata>): Getter for the model slot in a SplitTypeRdata class
`model<-`(<SplitTypeRdata>): Replacement of model slot in a SplitTypeRdata object
`model<-`(): Generic function for replacement of model slot in a class
model(): Generic function for getting the model slot in a class
permutations(<SplitTypeRdata>): Getter for the signatures slot in a SplitTypeRdata class
`permutations<-`(<SplitTypeRdata>): Replacement of permutations slot in a SplitTypeRdata object
`permutations<-`(): Generic function for replacement of permutations slot in a class
permutations(): Generic function for getting the permutations slot in a class
plotDensityWithUpscalingSamplesBimodal(): Graph both the alternative and the signature distributions obtained for a specific signature
plotPermutationSamplesDistribution(): Graph showing both the alternative and the signature distributions obtained for a specific signature
plotPermutationSamplesNormal(): Graph the enrichment results as violin plots from the permutation step
runSubtypingBimodal(): Classification of heterogeneous biological samples based on gene signature lists using a mixture of two normal distributions
show(<SplitTypeRdata>): Show a summary of a SplitTypeRdata object
signatures(<SplitTypeRdata>): Getter for the signatures slot in a SplitTypeRdata class
`signatures<-`(<SplitTypeRdata>): Replacement of signatures slot in a SplitTypeRdata object
`signatures<-`(): Generic function for replacement of signatures slot in a class
signatures(): Generic function for getting the signatures slot in a class
signaturesDemo: Demonstration gene signatures for PDAC subtyping
splitTypeR-package splitTypeR: Transcriptomic classification using multimodal distributions
standardDeviation(<SplitTypeRdata>): Getter for the standardDeviation slot in a SplitTypeRdata class
`standardDeviation<-`(<SplitTypeRdata>): Replacement of the standardDeviation slot in a SplitTypeRdata object
`standardDeviation<-`(): Generic function for replacement of standardDeviation slot in a class
standardDeviation(): Generic function for getting the standardDeviation slot in a class
threshold(<SplitTypeRdata>): Getter for the threshold slot in a SplitTypeRdata class
`threshold<-`(<SplitTypeRdata>): Replacement of threshold slot in a SplitTypeRdata object
`threshold<-`(): Generic function for replacement of threshold slot in a class
threshold(): Generic function for getting the threshold slot in a class
upscaling(<SplitTypeRdata>): Getter for the upscaling slot in a SplitTypeRdata class
`upscaling<-`(<SplitTypeRdata>): Replacement of the upscaling slot in a SplitTypeRdata object
`upscaling<-`(): Generic function for replacement of the upscaling slot in a class
upscaling(): Generic function for getting the upscaling slot in a class