grab.window: grab.window

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

grab.window

Description

helper function for adjusting the window around range of interest

if range falls within a complex event, then return the event footprint if gene is amplified but not in a complex event but is in a complex amplicon: - return amplicon if gene is not in a complex event OR in a complex amplicon: - return the range of the node(s) containing the gene

Usage

grab.window(
  gr,
  complex.fname,
  amp.thresh = 4,
  ploidy = 2,
  ev.types = c(),
  return.type = "data.table"
)

Arguments

gr	(GRanges)
complex.fname	(character)
amp.thresh	(numeric)
ploidy	(numeric)
ev.types	(character) list of acceptable event types (try to exclude simple events)
return.type	(character) one of "data.table" or "GRanges"

Value

data.table with node.fp, amp.fp, and ev.fp for node, event, and amplicon footprints

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