Bayes Factor for all targets, not only the cnv calls

vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

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Bayes Factor for all targets, not only the cnv calls #34

Closed vinzenzmay closed 3 years ago

vinzenzmay commented 3 years ago

Hi, do you have an idea how I could calculate the BF for all exons (that they are not a cnv/ are a cnv)? You wrote (p. 7):

It is in fact the log10 of the likelihood ratio of data for the CNV call divided by the null (normal copy number)

I see that the all.exons object has a member "likelihood", "expected", "reference", "test". Is it possible to get the BF scores from these values?

Thank you, Vinzenz

vinzenzmay commented 3 years ago

The class definition held the necessary information to get the scores from all.exons: e.g. for deletions: signif( log10(exp(1))*(all.exons@likelihood[i,1] - all.exons@likelihood[i,2]), 3)

Greetings, Vinzenz