I have two data files with the following columns: File 1, CGH_Probe_Table: Probe Name, Chromosome, Start, Stop, Feature Number, Log Ratio. File 2, SNP_Probe_Table: SNP ID, Probe Name, Chromosome, SNP Position, Feature number, Genotype.
My ultimate goal is to call copy numbers using this data, as well as do some grouping/segmenting of genic regions to find copy number change boundaries.. I am fairly new to this, so I would appreciate any help on how to calculate b-allele frequency (if possible, I don't think I have enough info in my files to do this), calling copy numbers based on logR2 while also segmenting areas of like copy numbers. Thanks!
R package Dnacopy and its CBS algorithm can solve it