predictSomatic {PureCN} | R Documentation |
This function takes as input the output of a runAbsoluteCN
run
and provides SNV posterior probabilities for all possible states.
predictSomatic(res, id = 1, return.vcf = FALSE)
res |
Return object of the |
id |
Candidate solutions to be analyzed. |
return.vcf |
Returns an annotated |
A data.frame
or CollapsedVCF
with SNV state posterior
probabilities.
Markus Riester
data(purecn.example.output) # the output data was created using a matched normal sample, but in case # no matched normal is available, this will help predicting somatic vs. # germline status purecnSnvs <- predictSomatic(purecn.example.output) # Prefer GRanges? purecnSnvs <- GRanges(predictSomatic(purecn.example.output)) # write a VCF file purecnVcf <- predictSomatic(purecn.example.output, return.vcf=TRUE) writeVcf(purecnVcf, file = "Sample1_PureCN.vcf")