mskcc / facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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What does the size of mafR which in cncf explain? #74

Open Jingjiao-ma opened 6 years ago

Jingjiao-ma commented 6 years ago

hi, In the output cncf file, the column mafR , what does the size of the number mean?Is there a relationship between the size of the number and the imbalance of allele?

thank you

veseshan commented 6 years ago

mafR is the method of moments estimate of the square of log-odds-ratio from the 2x2 table obtained from tumor-normal by ref-alt cross-tabulation. So close to zero means the alleles are in balance. For total and minor copy numbers of (tcn, lcn) at cellular fraction cf the odds-ratio is {1+(tcn-lcn-1)cf}/{1+(lcn-1)cf}.