identifyKataegis: Identify Kataegis events in SNV mutation data

In shaghayeghsoudi/DPclust3p_Customised: Dirichlet Process Clustering Pre-Processing Package

Identify Kataegis events in SNV mutation data

Description

Identify Kataegis events in SNV mutation data

Usage

identifyKataegis(
  samplename,
  dpInfile,
  outdir = ".",
  gamma_param = 25,
  kmin = 2,
  kataegis.threshold = NA,
  minMuts = 6,
  logScale = F,
  makePlots = F,
  removeFromDPin = F
)

Arguments

samplename	Samplename used when writing output files
dpInfile	A DP input file
outdir	Directory where output will be written
gamma_param	Gamma parameter to be used for segmentation
kmin	Kmin parameter to be used for segmentation
kataegis.threshold	Intermutation distance, if NA will be set to: (a) 900000 > SNVs: 100, (b) 500000 > SNVs: 250, (c) 100000 > SNVs, (d) otherwise 1000 (Default NA)
minMuts	Minimum number of mutations within kataegis.threshold to call Kataegis
logScale	Transform intermutation distance to logscale
makePlots	Make a figure for each Kataegis event
removeFromDPin	Remove SNVs identified as part of a Kataegis event from the DP input file

Author(s)

dw9

shaghayeghsoudi/DPclust3p_Customised documentation built on March 18, 2022, 5:28 a.m.