ccf_annotate_maf: Estimate CCFs of somatic mutations

In mskcc/facets-suite: Functions to run and parse output from FACETS

Estimate CCFs of somatic mutations

Description

Based on FACETS data, infer cancer-cell fraction (CCF) for somatic mutations in a sample.

Usage

ccf_annotate_maf(maf, segs, purity, algorithm = c("em", "cncf"))

Arguments

maf	Input MAF file.
segs	FACETS segmentation output.
purity	Sample purity estimate.
algorithm	Choice between FACETS em and cncf algorithm.

Value

MAF file annotated with clonality estimates for each mutation, where the following column prefixes are used:

• ccf_Mcopies*: Inferred CCF if mutation is on the major allele.

• ccf_1copy*: Inferred CCF if mutation exists in one copy.

• ccf_expected_copies*: Inferred CCF if mutation exists in number of copies expected from observed VAF and local ploidy.

mskcc/facets-suite documentation built on Sept. 13, 2022, 4:14 a.m.