PureCN (version 1.0.3)

predictSomatic: Predict germline vs. somatic status

Description

This function takes as input the output of a runAbsoluteCN run and annotates variants more correctly as germline vs. somatic by inferring maternal and paternal chromosome numbers.

Usage

predictSomatic(res, id = 1, cutoff = 0.1)

Arguments

res

Return object of the runAbsoluteCN() function.

id

Candidate solutions to be analyzed. id=1 will analyze the maximum likelihood solution.

cutoff

Exclude maternal/paternal chromosome number in segment if posterior probability is lower than cutoff.

Value

• A data.frame with adjusted SNV state posterior probabilities.

Examples

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
purecn.snvs <- predictSomatic(purecn.example.output)

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