VCFsToID115CatalogsAndPlotToPdf: Read a list of vcfs and plot ID115 catalogs as pdf

In steverozen/ICAMSxtra: ICAMSxtra

Description

Read a list of vcfs and plot ID115 catalogs as pdf

Usage

VCFsToID115CatalogsAndPlotToPdf(
  list.of.vcfs,
  ref.genome,
  region = "unknown",
  flag.mismatches = 0,
  file,
  ylim = NULL
)

Arguments

list.of.vcfs	List of in-memory ID VCFs. The list names will be the sample ids in the output catalog.
ref.genome	A ref.genome argument as described in ICAMS.
region	A character string acting as a region identifier, one of "genome", "exome".
flag.mismatches	Optional. If > 0, then if there are mismatches to references in the ID (insertion/deletion) VCF, generate messages showing the mismatched rows and continue. Otherwise stop if there are mismatched rows. See AnnotateIDVCF for more details.
file	The name of the PDF file to be produced.
ylim	Has the usual meaning. Only implemented for SBS96Catalog and IndelCatalog.

steverozen/ICAMSxtra documentation built on Feb. 9, 2022, 7:01 a.m.