cn.plot: cn.plot

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

cn.plot

Description

Creates .png files corresponding to gTrack plots for each amplified/deleted gene

Usage

cn.plot(
  drivers.fname = NULL,
  complex.fname = NULL,
  cvgt.fname = "./coverage.gtrack.rds",
  gngt.fname = "./data/gt.ge.hg19.rds",
  agt.fname = NULL,
  server = "",
  pair = "",
  ev.types = c("qrp", "tic", "qpdup", "qrdel", "bfb", "dm", "chromoplexy",
    "chromothripsis", "tyfonas", "rigma", "pyrgo", "cpxdm"),
  amp.thresh = 2,
  ploidy = 2,
  pad = 0.5,
  height = 1000,
  width = 1000,
  outdir = "./",
  overwrite = TRUE,
  verbose = TRUE
)

Arguments

drivers.fname	text file with drivers + CN alterations + genomic locations
complex.fname	(character) output from complex event caller
cvgt.fname	(character) coverage gTrack file path
gngt.fname	(character) gencode gTrack file path
agt.fname	(character) allele gTrack file name
server	(character) path to gGnome.js server url
pair	(character) pair id
ev.types	(character) complex event types
amp.thresh	(default 2) amplicon CN threshold for plotting ## possibly compute and save separately?
ploidy	(default 2)
pad	(numeric) window padding in bp default 5e5
height	(numeric) plot height default 500
width	(numeric) plot width default 500
outdir	(character) where to save plots?
verbose	(logical) default TRUE

Value

data.table with columns id, plot.fname, and plot.link

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