process_loose_ends: process_loose_ends

In mskilab/loosends: Classifying loose ends in gGraphs

process_loose_ends

Description

Annotate a set of loose ends (ranges) based on local assembly of adjacent read pairs

Usage

process_loose_ends(
  id = "",
  ranges = GRanges(),
  tbam = "/dev/null",
  nbam = "/dev/null",
  ref_dir = "/dev/null",
  outdir = "./",
  read_pad = 5000,
  assembly_pad = 1000,
  verbose = FALSE
)

Arguments

id	(character) sample ID
ranges	(GRanges)
tbam	(character) path to tumor bam
nbam	(character) path to normal bam
ref_dir	(character) path to reference directory
outdir	(character) directory for storing outputs
read_pad	(numeric) default 5000
assembly_pad	(numeric) default 1000
verbose	(logical) default TRUE

Value

list with two items

• call

• contigs

• support

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