read_support_wrapper: read_support_wrapper

In mskilab/loosends: Classifying loose ends in gGraphs

read_support_wrapper

Description

read_support_wrapper

Usage

read_support_wrapper(
  le.dt = data.table(),
  reads.dt = data.table(),
  contigs.dt = data.table(),
  id = "",
  pad = 5000,
  ref.bwa = NULL,
  ref.fasta = NULL,
  bowtie = FALSE,
  outdir = ".",
  verbose = FALSE
)

Arguments

le.dt	(full output from prep_loose_ends)
reads.dt	(full output from loose_reads_wrapper)
contigs.dt	($filtered.contigs from call_loose_end)
id	(character) sample id
pad	(numeric) window for getting supporting reads
ref.bwa	(human output from grab_ref_obj)
ref.fasta	(character) path to fasta if using bowtie
bowtie	(logical) default FALSE
outdir	(character) dirname for temporary files
verbose	(logical)

Value

data.table with columns

• leix

• loose.end

• contig.qname

• tumor.count

• normal.count

• total.count

• tumor.frac

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