detectActiveSignatures: Get a list of signatures active in a sample

Description Usage Arguments Value

View source: R/TrackSig.R

Description

detectActiveSignatures determines what signatures are active above an activity threshold, from a list of signature definintions. To do this, a multinomial mixture model of signature activities is fit to the collection of all mutations in the sample.

Usage

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detectActiveSignatures(
  vcfFile,
  cnaFile = NULL,
  purity = 1,
  threshold = 0.05,
  prior = NULL,
  binSize = 100,
  referenceSignatures = alex_merged,
  refGenome = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
)

Arguments

vcfFile

path to variant calling format (vcf) file

cnaFile

path to copy number abberation (cna) file. If not provided, all copy numbers default to 2.

purity

number between 0 and 1 of the percentage of cells in the sample that are cancerous

threshold

minimum activity level that signature must have to be detected

prior

prior on the likelihood of observing a given signature (must match signatures present in referenceSignatures)

binSize

number of mutations per bin (default 100)

referenceSignatures

dataframe containing definitions of mutational signatures.

refGenome

BSgenome to use as reference

Value

Names of signatures active in sample.


morrislab/TrackSigFreq documentation built on June 29, 2020, 5:13 a.m.