gallery.wrapper: gallery.wrapper

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

gallery.wrapper

Description

wrapper function to prep input for SlickR

Usage

gallery.wrapper(
  complex.fname = NULL,
  background.fname = "/data/sv.burden.txt",
  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"),
  pad = 5e+05,
  height = 1000,
  width = 1000,
  outdir = "./"
)

Arguments

complex.fname	(character)
background.fname	(character) text file with event burdens (default sv.burden.txt)
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
pad	(numeric) window padding in bp default 5e5
height	(numeric) plot height default 1000
width	(numeric) plot width default 1000
outdir	(character) where to save plots
cgcgt.fname	(character) CGC gTrack file path

Value

data.table with columns from complex and additionally plot.fname and plot.link

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