pscnseq_pscbs: Runs Parent-Specific Copy-Number Segmentation (PSCBS) on a...

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

Description

Runs Parent-Specific Copy-Number Segmentation (PSCBS) on a Dataset

Usage

pscnseq_pscbs(dataset, organism, chrs, samples, binsize, 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’.
binsize	(integer or numeric) The bin size (in basepairs) used for binning reads into bins that then are passed to the segmentation method.
verbose	(logical) If TRUE, then verbose output is produced, otherwise not.

Value

(character vector) Pathnames to ‘*,PairedPSCBS.rds’ files holding PSCBS::segmentByPairedPSCBS results.

See Also

This function uses PSCBS::segmentByPairedPSCBS().

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