grab_looseread_params: grab_looseread_params

In mskilab/loosends: Classifying loose ends in gGraphs

grab_looseread_params

Description

Grab ranges and qnames of reads near loose ends + their mates (Including ranges for split reads)

Usage

grab_looseread_params(
  gr = GRanges(),
  bam = character(),
  mask = "/dev/null",
  pad = 5000,
  mate_pad = 150,
  verbose = FALSE
)

Arguments

gr	(GRanges) stranded GRanges representing loose ends
bam	(character) path to bam file
mask	(character) path to GRanges to excluded reads
pad	(numeric) pad around loose ends
mate_pad	(numeric) pad around mate windows
verbose	(logical)

Value

list with names:

• $ranges (GRanges of windows)

• $qnames (character vector of loose read qnames)

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