Question: In FACETS, what does the mafR value represent?
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gravatar for sviatoslav.kendall
22 months ago by
United States
sviatoslav.kendall440 wrote:

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.

cnv • 635 views
ADD COMMENTlink modified 11 months ago by bruce.moran410 • written 22 months ago by sviatoslav.kendall440
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gravatar for bruce.moran
11 months ago by
bruce.moran410
Ireland
bruce.moran410 wrote:

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.

ADD COMMENTlink written 11 months ago by bruce.moran410
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