I am using cn.mops Bioconductor package for analysis of CNV in exome-seq data. But whever I run
referencecn.mops, the program throws an error:
Error in strand(input) :
error in evaluating the argument 'x' in selecting a method for function 'strand': Error: object 'input' not found
I tried changing strand information manually, created GRanges object manually , but nothing works. But, if I use the same GRanges object with the function cn.mops - it works flawlessly without any error.
Any help is appreciated.
edit: My Command -
aml.counts is a GRanges object with 3 meta data column representing the read counts for bait regions. 1st meta data column is for control where 2nd and 3rd are for tumor. I have also tried with single case (tumor), but it gives me the same error.