grab_distal_breakends: grab_distal_breakends

In mskilab/loosends: Classifying loose ends in gGraphs

grab_distal_breakends

Description

Grab candidate distal breakends based on tumor-specificity

If there are tumor-specific breakends: If there are MAPQ = 60 breakends all within 1kbp: returns a single breakend (the first one) If there are MAPQ = 60 breakends but not within 1 kbp: return MAPQ = 60 breakends Otherwise, return all breakends

Usage

grab_distal_breakends(
  bps,
  mapq.thresh = 60,
  specificity.thresh = 0.05,
  pad = 1000
)

Arguments

bps	(data.table) data.table representing breakpoints coercible to GRanges. bps needs to have columns mapq, tumor.count, and normal.count representing supporting barcodes for that contig.
mapq.thresh	(default 60)
specificity.thresh	(numeric) cutoff for tumor-specific contigs
pad	(numeric) default 1 kbp

Value

a data.table with filtered breakends and additional metadata columns

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.