getSubtypeProbes: Retrieving outlier genes from a group of related samples

In DavisLaboratory/oppar: Outlier profile and pathway analysis in R

Description

Returns a list of genes that are outlier in a group of samples, such as samples from the same subtype.

Usage

getSubtypeProbes(profileMatrix, sample.names)

## S4 method for signature 'matrix,nuchar'
getSubtypeProbes(profileMatrix, sample.names)

## S4 method for signature 'OPPARList,nuchar'
getSubtypeProbes(profileMatrix, sample.names)

Arguments

profileMatrix	A matrix of 0,1 and -1, representing outlier genes in samples. Also an object of type OPPARList.
sample.names	A character vector containing sample names, or a numeric vector containing the indices of the samples.

Value

A list of lists. The sub-lists are up-regulated outlier genes, and down-regulated outlier genes.

Methods (by class)

• 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

Examples

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)

DavisLaboratory/oppar documentation built on May 6, 2019, 1:56 p.m.