pscnseq_sequenza: Estimates Cellularity and Ploidy and Copy-Number Calls using...

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

Description

Estimates Cellularity and Ploidy and Copy-Number Calls using Sequenza

Usage

pscnseq_sequenza(
  dataset,
  organism,
  chrs,
  samples,
  fasta,
  gcbase,
  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’.
verbose	(logical) If TRUE, then verbose output is produced, otherwise not.

Value

A aroma.seq::SeqzFileSet.

See Also

This function uses aroma.seq::pileup2seqz().

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