grab.agtrack: grab.agtrack

In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

grab.agtrack

Description

returns allele gtrack given sites.txt from het pileup

Usage

grab.agtrack(
  agt.fname = NULL,
  min.frac = 0.2,
  max.frac = 0.8,
  purity = NULL,
  ploidy = NULL,
  major.col = "red",
  minor.col = "blue",
  max.ranges = 10000,
  lwd.border = 0.2,
  name = "SNP",
  ...
)

Arguments

agt.fname	(character) path to sites.txt
min.frac	(numeric) between 0 and 1, min frequency in normal to count as het site
max.frac	(numeric) between 0 and 1, max frequency in normal to count as het site
purity	(numeric)
ploidy	(numeric)
major.col	(character) major allele color
minor.col	(character) minor allele color
max.ranges	(numeric) gTrack param
lwd.border	(numeric)
name	(character) gTrack name
...	additional args to be passed to gTrack

Value

allele gTrack

mskilab/casereport documentation built on Oct. 19, 2022, 3 a.m.