summaryCopa: Create Summary Showing Top Gene Pairs
In copa: Functions to perform cancer outlier profile analysis.

Description Usage Arguments Value Author(s) References Examples

View source: R/copa.R

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.

1	summaryCopa(copa, pairnum, lib = NULL)

`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

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.

James W. MacDonald <jmacdon@u.washington.edu>

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

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