summaryCopa {copa} | R Documentation |
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.
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@med.umich.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) }