background: Randomly choose background genes.

In RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis

Description

background returns background genes for judging the quality of the cleaning. These genes are supposed to represent the majority of genes. The positive control and negative control genes should be excluded.

Usage

background(Y, nBG, exclude, nc_index)

Arguments

Y	A matrix of gene expression values or an object of the class simulateGEdata.
nBG	An integer setting the number of background genes.
exclude	A vector of indices of genes to exclude.
nc_index	A vector of indices of negative controls (also excluded from being background genes).

Value

background returns a vector of randomly chosen indices.

Author(s)

Saskia Freytag

Examples

Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1, 
250, 100, intercept=FALSE, check.input=FALSE)  
background(Y, nBG=20, exclude=1:100, nc_index=251:500)

RUVcorr documentation built on Nov. 8, 2020, 5:10 p.m.