getSampleOutlier {oppar} | R Documentation

## Retrieving outlier genes in samples

### Description

Returns a list of outlier genes for each given sample

### Usage

    getSampleOutlier(profileMatrix, sample.name)

    ## S4 method for signature 'matrix,nuchar'
    getSampleOutlier(profileMatrix, sample.name)

    ## S4 method for signature 'OPPARList,nuchar'
    getSampleOutlier(profileMatrix, sample.name)

### Arguments

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

### Value

A list of lists. For each given sample, the fuction return up-regulated and down-regulated outlier genes.

### Methods (by class)

- `profileMatrix = matrix,sample.name = nuchar`: A method for getSampleOutlier

- `profileMatrix = OPPARList,sample.name = nuchar`: A method for getSampleOutlier

### 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)
    # 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"))

[Package oppar version 1.20.0 Index]