pp_plot: pp_plot

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

pp_plot

Description

pp_plot

Usage

pp_plot(
  jabba_rds = NULL,
  cov.fname = NULL,
  hets.fname = NULL,
  allele = FALSE,
  field = NULL,
  plot.min = -2,
  plot.max = 2,
  scatter = FALSE,
  bins = 500,
  height = 800,
  width = 800,
  output.fname = "./plot.png",
  purity = NA,
  ploidy = NA,
  verbose = FALSE
)

Arguments

jabba_rds	(character) JaBbA output
cov.fname	(character) path to coverage GRanges (supply if allele = FALSE)
hets.fname	(character) path to sites.txt (supply if allele = TRUE)
allele	(logical) allelic CN? default FALSE
field	(character) default ratio if allele is FALSE and count if allele is TRUE
plot.min	(numeric) minimum CN default -2
plot.max	(numeric) max CN (factor times ploidy) default 2
scatter	(logical) default FALSE
bins	(numeric) number of histogram bins default 500
height	(numeric) plot height
width	(numeric) plot width
output.fname	(character) path of output directory
purity	(numeric) if not provided then the value is read from the input JaBbA
ploidy	(numeric) if not provided then the value is read from the input JaBbA
verbose	(logical)

Details

create histogram of estimated copy number given purity and ploidy

Value

output.fname

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