ReadEMuCatalog: Read Catalog files in EMu format.

In WuyangFF95/SynSigEval: Evaluate Results of Mutational Signature Analysis Software on Synthetic Spectra Created by Package SynSigGen

Read Catalog files in EMu format.

Description

Read Catalog files in EMu format.

Usage

ReadEMuCatalog(
  cat,
  mutTypes,
  sigOrSampleNames,
  region = "unknown",
  catalog.type = "counts.signature"
)

Arguments

cat	A tab-delimited catalog text file in EMu format; or a EMu formatted matrix or data.frame.
mutTypes	Types of mutations. They are usually from an ICAMS:::catalog.row.header object.
sigOrSampleNames	If input file is a counts signature file (catalog.type == "counts.signature"), signature names should be provided. If input file is a counts spectra file (catalog.type == "counts"), names of samples should be provided.
region	Catalog region. Can be a specific genomic or exomic region, or "unknown". Default: "unknown"
catalog.type	Is the catalog a signature catalog, or a spectrum catalog? Default: "counts"

Value

a catalog matrix in ICAMS format.

WuyangFF95/SynSigEval documentation built on Sept. 18, 2022, 11:41 a.m.