matrixToGenelist {ADAPTS}

Make a GSVA genelist

Description

Provide a gList and signature matrix with matched cell types to get signatures gene lists for GSVA and similar algorithms. gList=NULL select highest genes for each cell type, minimum of 3.

Usage

matrixToGenelist(sigMat, gList = NULL)

Arguments

sigMat

A signature matrix such as from ADAPTS::AugmentSigMatrix()

gList

A list of prioritized genes such as from ADAPTS::gListFromRF() (DEFAULT:NULL)

Value

A list of genes for each cell types musually in sigMat and gList

Examples

library(ADAPTS)
ct1 <- runif(1000, 0, 100)
ct2 <- runif(1000, 0, 100)
dataMat <- cbind(ct1, ct1, ct1, ct1, ct1, ct1, ct2, ct2, ct2, ct2)
rownames(dataMat) <- make.names(rep('gene', nrow(dataMat)), unique=TRUE)
noise <- matrix(runif(nrow(dataMat)*ncol(dataMat), -2, 2), nrow = nrow(dataMat), byrow = TRUE)
dataMat <- dataMat + noise
gList <- ADAPTS::gListFromRF(trainSet=dataMat, oneCore=TRUE)
newSigMat <- ADAPTS::buildSeed(trainSet=dataMat, plotIt=FALSE)
geneLists <- matrixToGenelist(sigMat=newSigMat, gList=gList)