Reference

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

expNormalCountsDemo

A small normalized expected gene counts matrix for 30 patients generated to be used as a demonstration set in this package.

getGeneSignatures()

Return the selected gene list signatures

getGeneSignaturesNames()

List the names of the available signatures

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

permutations(<SplitTypeRdata>)

Getter for the signatures slot in a SplitTypeRdata 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 TODO

runSubtypingBimodal()

Classification of heterogeneous biological samples based on gene signature lists using a mixture of two normal distributions

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

A short collection of published gene signatures primarily focuses on PDAC classification for patient-derived organoids (PDO). While the signatures are accurate, this list is mainly compiled for demonstration purposes.

splitTypeR-package splitTypeR

Transcriptomic classification using multimodal distributions

print(<splitTypeResults>)

Print a splitTypeResults object

standardDeviation(<SplitTypeRdata>)

Getter for the standardDeviation slot in a SplitTypeRdata class

standardDeviation()

Generic function for getting the standardDeviation slot in a class

upscaling(<SplitTypeRdata>)

Getter for the upscaling slot in a SplitTypeRdata class

upscaling()

Generic function for getting the upscaling slot in a class