ICAMS (version 2.0.10)

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", names.of.VCFs = NULL, tumor.col.names = NA)

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.

names.of.VCFs

Character vector of names of the VCF files. The order of names in names.of.VCFs should match the order of VCF file paths in files. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) in files and file paths without extensions (and the leading dot) will be used as the names of the VCF files.

tumor.col.names

Character vector of column names in VCFs which contain the tumor sample information. The order of names in tumor.col.names should match the order of VCFs specified in files. If tumor.col.names is equal to NA(default), this function will use the 10th column in all the VCFs to calculate VAFs. See GetMutectVAF for more details.

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.

Comments

To add or change attributes of the catalog, you can use function attr. For example, attr(catalog, "abundance") <- custom.abundance.

Details

This function calls VCFsToSBSCatalogs, VCFsToDBSCatalogs and VCFsToIDCatalogs

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Mutect.GRCh37.vcf",
                      package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catalogs <- MutectVCFFilesToCatalog(file, ref.genome = "hg19", 
                                      trans.ranges = trans.ranges.GRCh37,
                                      region = "genome")}
# }