I am going to do some analysis on Illumina SNP data.

I am using illuminaio BioC pacakge to parse my .idat files and also the manifest file (.bpm) and then I will proceed to use DNAcopy to do the CNA analysis.

I am facing some problems when using the command readBPM(). The readBPM() function doesn't return chromosome and position that are needed for DNAcopy's CNA function.

Can someone help me? How and where could I get and extract the chromosome and position using readBPM() function?

Thank you.

Regards,
jingxian