error in function runPairedSampleAnalysis()

[lida-R]

Hello,

I have tried the copyCat and function runPairedSampleAnalysis() for CNV analysis but got below error.

[1] "inferred bin size: 10000"
[1] "Can't infer read length from window file headers"
[1] "and read length was not specified in setParams()"
[1] "correct one of these to proceed"
Error in getWindowBins(rdo) :

Do you have any thoughts?

Thanks,
Lida

[chrisamiller]

You can either alter the setParams() command within that block to explicitly state the bin size, or you can alter the header of your bins file such that it's something like counts.151. Copycat will infer that everything after the final period is a bin size for that column.