I've been working with some copy number data produced using FACETS and I'm just wondering if anyone knows what the "mafR" values represent. I've read the documentation but found nothing explaining what this value means.
Probably a bit old but I am working through this method, so:
?procSample ... 'mafR’ the log-odds-ratio summary for the segment
This represents the ratio of counts of heterozygous sites in the tumour/normal pair (log-ratio is the ratio of total counts in tumour/normal pair). The idea behind this is that the variant/minor/'B' allele frequency (where I believe the 'mafR' name comes from: minor allele frequency ratio) can tell you if a region has loss of heterozygosity, even when it is copy-number neutral.