pscnseq_mpileup: Produces "pileup" Output Files from Read Alignments (BAM...

In HenrikBengtsson/CostelloPSCNSeq: Parent-Specific Copy-Number Estimation Pipeline using HT-Seq Data

Description

Produces "pileup" Output Files from Read Alignments (BAM Files)

Usage

pscnseq_mpileup(
  dataset,
  organism,
  chrs,
  samples,
  fasta,
  gcbase,
  bam_pattern = NULL,
  verbose = FALSE
)

Arguments

dataset	(character) The name of the dataset as on file.
organism	(character) The name of the organism as on file.
chrs	(character vector) The name of the chromosomes to be processed, e.g. c("1", "2", "X").
samples	(character) Pathname to a tab-delimited sample specification file, typically named ‘*.tsv’, e.g. ‘samples.tsv’.
fasta	(character) The pathname to the FASTA reference file, typically named ‘*.fa’ or ‘*.fasta’, e.g. ‘hg19.fa’.
gcbase	(character) The pathname to the FASTA reference file, typically named ‘*.txt.gz’, e.g. ‘hg19.gc50Base.txt.gz’.
bam_pattern	(character; optional) Regular expression to identify subset of BAM files to be processed. If NULL (default), then BAM files matching .bwa.realigned.rmDups(|.recal)(|.bam)$ are included.
verbose	(logical) If TRUE, then verbose output is produced, otherwise not.

Value

A aroma.seq::MPileupFileSet.

See Also

This function uses aroma.seq:mpileup().

HenrikBengtsson/CostelloPSCNSeq documentation built on Feb. 28, 2021, 5:49 p.m.