I have log R ratios and beta allele frequencies from Affy6 data. I've used the LRR with the R package fastseg to segment the data. The problem is, I need copy number calls and it appears that fastseg just gave me segmentation means for the LRR and fancy plots. Can I use this to estimate copy number integers or do I need to start back at square one with my LRR & BAF using a different package? After segmenting with fastseg, I have ranges, num.mark (integer), seg.mean (numeric), startRow (integer), and endRow(integer). I've looked into PennCNV & cn.mops but I don't know much about them.
Any guidance would be greatly appreciated.