getVerhaakSubtypes: Get Ovarian Cancer Subtypes (as defined by Verhaak et al....

In bhklab/MetaGx: R package for meta-analysis of breast cancer gene expressions

Usage

getVerhaakSubtypes(eset)

Arguments

eset

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (eset) 
{
    supplementary.data <- read.xls("../inst/extdata/JCI65833sd1.xls", 
        sheet = 7, skip = 1)
    genesets <- lapply(levels(supplementary.data$CLASS), function(y) as.character(supplementary.data[supplementary.data$CLASS == 
        y, 1]))
    names(genesets) <- levels(supplementary.data$CLASS)
    gsva.out <- gsva(exprs(eset), genesets, method = "ssgsea", 
        min.sz = 10, tau = 0.75, parallel.sz = 1)
    gsva.out <- t(gsva.out)
    subclasses <- as.factor(apply(gsva.out, 1, function(x) colnames(gsva.out)[which.max(x)]))
    pData(eset) <- data.frame(pData(eset), Verhaak.subtypes = subclasses)
    return(list(Annotated.eset = eset, gsva.out = gsva.out))
  }

bhklab/MetaGx documentation built on May 12, 2019, 8:25 p.m.