Hi All, I am using copywriteR to identify somatic copy number variants in a matched experiment in which I have normal and tumor. I runned copywriteR just fine following the R vignette. At the end of the process after I have called plotCNA function I can load the results that are in the segment.Rdata object.
Here if I understood well in the column seg.mean have for each segment the Log2ratio value of each segment. Now, my question is, how I can define what is amplified or deleted? If I understood well reading around, doing 2^log2ratio should give me number of copies. But is it possible to assign a pvalue for each segment that tells how much that segment should be altered? Or how can I selected a threshold in log2ratio to define what is altered and what not?
Thank you in advance for any help and clarification.
> head(segment.CNA.object$output) ID chrom loc.start loc.end num.mark seg.mean 1 log2.tum.bam.vs.log2.normal.bam 1 825000.5 41575000 787 -0.1760 2 log2.tum.bam.vs.log2.normal.bam 1 41625000.5 93175000 1016 0.3496 3 log2.tum.bam.vs.log2.normal.bam 1 93225000.5 93275000 2 2.3676 4 log2.tum.bam.vs.log2.normal.bam 1 93325000.5 93475000 4 0.7452 5 log2.tum.bam.vs.log2.normal.bam 1 93525000.5 94275000 16 0.1227 6 log2.tum.bam.vs.log2.normal.bam 1 94325000.5 121575000 505 -0.1780