getSubtypeProbes {oppar} | R Documentation |
Returns a list of genes that are outlier in a group of samples, such as samples from the same subtype.
getSubtypeProbes(profileMatrix, sample.names) ## S4 method for signature 'matrix,nuchar' getSubtypeProbes(profileMatrix, sample.names) ## S4 method for signature 'OPPARList,nuchar' getSubtypeProbes(profileMatrix, sample.names)
profileMatrix |
A matrix of 0,1 and -1, representing outlier genes in samples.
Also an object of type |
sample.names |
A character vector containing sample names, or a numeric vector containing the indices of the samples. |
A list of lists. The sub-lists are up-regulated outlier genes, and down-regulated outlier genes.
profileMatrix = matrix,sample.names = nuchar
: A method for getSubtypeProbes with signature profileMatrix = matrix
and sample.names = nuchar
profileMatrix = OPPARList,sample.names = nuchar
: A method for getSubtypeProbes with signature profileMatrix = OPPARList
and sample.names = nuchar
data(GSE46141) library(Biobase) group <- sapply(pData(bcm)$source_name_ch1, function(x){ ifelse(x == "breast",0,1)}) group <- factor(group) bcm.opa <- opa(bcm,group=group) # extracting liver samples index <- which(pData(bcm)$source_name_ch1 == "liver") samples <- rownames(pData(bcm)[index,]) samples <- match(samples, colnames(bcm.opa$profileMatrix)) samples <- Reduce(c,samples) # liver subtype outlier profile liver.subtype.outlier <- getSubtypeProbes(bcm.opa, samples)