Question: In FACETS, what does the mafR value represent?
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gravatar for sviatoslav.kendall
11 months ago by
United States
sviatoslav.kendall420 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 • 326 views
ADD COMMENTlink modified 11 days ago by bruce.moran240 • written 11 months ago by sviatoslav.kendall420
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gravatar for bruce.moran
11 days ago by
bruce.moran240
Ireland
bruce.moran240 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 days ago by bruce.moran240
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