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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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(CNLR_MEDIAN) or (CNLR_MEDIAN - dipLogR) #6

Closed ahwanpandey closed 5 years ago

ahwanpandey commented 5 years ago

Hi again,

I was wondering what the correct value to use is for the log-ratio of a segment. I believe the tcn and lcn values have been corrected for ploidy and purity but logR values are not?

These log ratio values would be used for segment data visualization in IGV as well as for GISTIC analyses, and perhaps also to assign a log-ratio value to a gene.

Thanks!

dariober commented 5 years ago

I think (CNLR_MEDIAN - dipLogR) is usually more meaningful. About ploidy correction see https://github.com/mskcc/facets/issues/73

ahwanpandey commented 5 years ago

Thank you for the directions!