TrackSig: Determine an evolutionary trajectory.

Description Usage Arguments

View source: R/TrackSig.R

Description

TrackSig will take an input VCF file and corresponding annotation, and determine an eveolutionary trajectory for the sample, based on changepoints found using the PELT segmentation algorithm.

Usage

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TrackSig(
  vcfFile,
  activeInSample,
  cnaFile = NULL,
  purity = 1,
  sampleID = NULL,
  referenceSignatures = TrackSig:::alex_merged,
  scoreMethod = "SigFreq",
  binSize = 100,
  nCutoff = 10000,
  desiredMinSegLen = 1,
  refGenome = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
)

Arguments

vcfFile

path to variant calling format (vcf) file

activeInSample

list of signatures names to fit the exposures of. All listed signatures must be present in the referenceSignatures dataframe.

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

sampleID

name to call sample. If none provided, name will be automatically drawn from the provided vcf file name.

referenceSignatures

dataframe containing definitions of mutational signatures.

scoreMethod

string to indicate what scoring method to apply when finding changepoints. Options are "Signature", "SigFreq" and "Frequency"

binSize

number of mutations per bin (default 100)

nCutoff

maximum number of total mutations to consider (samples with more than nCutoff muations will be down-sampled)

desiredMinSegLen

minimum number of mutations to include in a PELT segment (the desiredMinSegLen will be overridden if there are too few for accurate scoring)

refGenome

BSgenome to use as reference


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