copa (version 1.40.0)

summaryCopa: Create Summary Showing Top Gene Pairs

Description

This function can be used to output a data.frame containing the ID and optionally the gene symbol for the top gene pairs, based on the number of outliers.

Usage

summaryCopa(copa, pairnum, lib = NULL)

Arguments

copa

An object of class 'copa', resulting from a call to the copa function.

pairnum

The maximum number of outlier pairs to be output. A table can be output first using tableCopa

lib

For Affymetrix data that have an annotation package, this can be specified and the table will then also contain the gene symbol

Value

The output from this function is a data.frame with the number of outliers, the manufacturer identifiers, and optionally, the gene symbol for the genes.

References

Tomlins, SA, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005 Oct 28;310(5748):644-8.

Examples

if(interactive()){
library(Biobase)
data(sample.ExpressionSet)
cl <- abs(3 - as.numeric(pData(sample.ExpressionSet)[,2]))
tmp <- copa(sample.ExpressionSet, cl)
summaryCopa(tmp, 6)
}