scatterPlotCopa: Create scatterplots of interesting gene pairs
In copa: Functions to perform cancer outlier profile analysis.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/copa.R

This function allows one to create scatterplots of gene pairs that may be involved in recurrent gene fusion in cancer.

1	scatterPlotCopa(copa, idx, lib = NULL)

`copa`	An object of class 'copa', resulting from a call to the `copa` function
`idx`	A numeric vector listing the gene pairs to plot (e.g., idx = 1:3 will plot the first three gene pairs).
`lib`	If the underlying data are Affymetrix expression values, one can specify an annotation package and the plot labels will be extracted from the xxxSYMBOL environment. If `NULL`, the `row.names` of the gene expression matrix will be used.

Note that this function will output all the gene pairs in the idx vector without pausing. This can be controlled by either setting par(ask = TRUE), or by redirecting the output to a file (using e.g., pdf, ps, etc.).

This function is called solely for outputting plots. No values are returned.

James W. MacDonald

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)
scatterPlotCopa(tmp, 1)
}