pscnseq: Calling the Parent-Specific Copy-Number Pipeline Step by Step

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

Description

Calling the Parent-Specific Copy-Number Pipeline Step by Step

Usage

pscnseq(
  what = c("mpileup", "sequenza", "pscbs", "reports"),
  dataset = NULL,
  organism = NULL,
  chrs = NULL,
  samples = NULL,
  fasta = NULL,
  gcbase = NULL,
  bam_pattern = NULL,
  binsize = NULL,
  config = "config.yml",
  session_details = !interactive(),
  verbose = TRUE,
  ...
)

Arguments

what	(character) The step to be performed; in order, one of "mpileup", "sequenza", "pscbs", or "reports".
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.
binsize	(integer or numeric) The bin size (in basepairs) used for binning reads into bins that then are passed to the segmentation method.
config	(character) Pathname to YAML configuration file. If NULL, then the configuration file is skipped.
session_details	(logical) If TRUE, session details are reported before starting the processing and after it completed.
verbose	(logical) If TRUE, then verbose output is produced, otherwise not.
...	Not used.

Value

Returns what the called pscnseq_nnn() function returns, i.e. pscnseq_mpileup(), pscnseq_sequenza(), pscnseq_pscbs(), or pscnseq_reports().

Format of the samples file

The samples argument should specify the pathname to a TAB-delimited file that provide annotation data for the samples to be processed. This file should a row of TAB-delimited column headers followed rows of samples with corresponding, TAB-delimited cells. The samples file must provide columns Patient_ID, Sample_ID, and A0. Any other columns are ignored. This pipeline processes tumor-normal pairs. The pairs processed are inferred from (Patient_ID, Sample_ID). Specifically, for each unique Patient_ID, the sample entry with Sample_ID == "Normal" is used as the normal reference. There must only be such entry per patient. Each patient may have one or more tumor samples, which are identified as Sample_ID != "Normal".

For example, the below ‘samples.tsv’ file specifies two tumor-normal pairs Primary-v1 vs Normal and Primary-v2 vs Normal for one patient named Patient123. This file specifies also fields SF, Kit, and A0, which may be used in other pipelines but are all ignored by this pipeline.

Patient_ID      Sample_ID       SF      Kit     A0
Patient123      Normal  SF00121N        Xgen Exome Research Panel       X00001
Patient123      Primary-v1      SF00121-v1      Xgen Exome Research Panel       X00002
Patient123      Primary-v2      SF00121-v2      Xgen Exome Research Panel       X00003

This

Configuration File

The default arguments can be set in an YAML-formatted configuration file as given by argument config. The default is to look for a file named ‘config.yml’ in the current directory. To skip this file, specify config = NULL. An example of such a file is:

organism: Homo_sapiens
chromosomes: c(1:22, "X", "Y", "M")
fasta: annotationData/organisms/Homo_sapiens/GRCh37,hg19/UCSC/hg19.fa
gcbase: annotationData/organisms/Homo_sapiens/GRCh37,hg19/UCSC/hg19.gc50Base.txt.gz
dataset: CostelloP_2015-Exome,bwa,realigned,rmDups,recal
binsize: 100e3
samples: sampleData/samples.tsv

Specifying arguments via command-line options

The arguments can be overridden by command-line options, e.g. --organism=Homo_sapiens will take precedence of argument organism, which in turn will take precedent of what is specified in the configuration file.

How to call pipeline from the command line

Below is how you could run the pipeline step by step. The --args option tells Rscript that any options following should be passed as arguments to this function.

Rscript -e CostelloPSCNSeq::pscnseq --args --help
Rscript -e CostelloPSCNSeq::pscnseq --args --what=mpileup   # ~25 min
Rscript -e CostelloPSCNSeq::pscnseq --args --what=sequenza  # ~60 min
Rscript -e CostelloPSCNSeq::pscnseq --args --what=pscbs     #  ~5 min
Rscript -e CostelloPSCNSeq::pscnseq --args --what=reports   #  ~2 min

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