ICAMS (version 2.0.7)

MutectVCFFilesToCatalog: Create SBS, DBS and Indel catalogs from Mutect VCF files

Description

Create 3 SBS catalogs (96, 192, 1536), 3 DBS catalogs (78, 136, 144) and Indel catalog from the Mutect VCFs specified by files

Usage

MutectVCFFilesToCatalog(files, ref.genome, trans.ranges = NULL,
  region = "unknown")

Arguments

files

Character vector of file paths to the Mutect VCF files.

ref.genome

A ref.genome argument as described in ICAMS.

trans.ranges

a data.table which contains transcript range and strand information. Please refer to TranscriptRanges for more details.

region

A character string designating a genomic region; see as.catalog and ICAMS.

Value

A list of 3 SBS catalogs (one each for 96, 192, and 1536), 3 DBS catalogs (one each for 78, 136, and 144) and ID catalog. If trans.ranges = NULL, SBS 192 and DBS 144 catalog will not be generated. Each catalog has attributes added. See as.catalog for more details.

Details

This function calls VCFsToSBSCatalogs, VCFsToDBSCatalogs and VCFsToIDCatalogs

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Mutect.GRCh37.vcf",
                      package = "ICAMS"))
catalogs <- MutectVCFFilesToCatalog(file, ref.genome = "hg19", 
                                    trans.ranges = trans.ranges.GRCh37,
                                    region = "genome")
# }