getSubtypeProbes {oppar} | R Documentation

## Retrieving outlier genes from a group of related samples

### 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)

[Package oppar version 1.22.0 Index]