sv.plot: sv.plot

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

sv.plot

Description

Creates .png files corresponding to gTrack plots for each complex SV pattern

Usage

sv.plot(
  complex.fname = NULL,
  cvgt.fname = "./coverage.gtrack.rds",
  gngt.fname = "./data/gt.ge.hg19.rds",
  genes.gt.fname = NULL,
  agt.fname = NULL,
  server = "",
  pair = "",
  ev.types = c("qrp", "tic", "qpdup", "qrdel", "bfb", "dm", "chromoplexy",
    "chromothripsis", "tyfonas", "rigma", "pyrgo", "cpxdm"),
  pad = 5e+05,
  height = 1000,
  width = 1000,
  outdir = "./"
)

Arguments

complex.fname	(character) output from complex event caller
cvgt.fname	(character) coverage gTrack file path
gngt.fname	(character) gencode gTrack file path
genes.gt.fname	(character) CGC gTrack file path
agt.fname	(character) allele gTrack file name
server	(character) server url
pair	(character) pair id
ev.types	(character) complex event types
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?

Value

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

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