| getSampleOutlier {oppar} | R Documentation |
Returns a list of outlier genes for each given sample
getSampleOutlier(profileMatrix, sample.name) ## S4 method for signature 'matrix,nuchar' getSampleOutlier(profileMatrix, sample.name) ## S4 method for signature 'OPPARList,nuchar' getSampleOutlier(profileMatrix, sample.name)
profileMatrix |
A matrix of 0, -1 and 1 representing outlier genes in samples.
Also an object of type |
sample.name |
A character vector containing one or more sample names, or a numeric vector containing sample indices. |
A list of lists. For each given sample, the fuction return up-regulated and down-regulated outlier genes.
profileMatrix = matrix,sample.name = nuchar: A method for getSampleOutlier
profileMatrix = OPPARList,sample.name = nuchar: A method for getSampleOutlier
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)
# Outlier profile for sample "GSM1124929"
getSampleOutlier(bcm.opa, "GSM1124929")
# Also can use sample index, instead of sample name
getSampleOutlier(bcm.opa, 11)
# A vector of sample names/indices are accepted as well
getSampleOutlier(bcm.opa, c(1,2))
getSampleOutlier(bcm.opa, c("GSM1124929","GSM1124941"))