ICAMS (version 2.0.7)

VCFsToSBSCatalogs: Create SBS catalogs from SBS VCFs

Description

Create a list of 3 catalogs (one each for 96, 192, 1536) out of the contents in list.of.SBS.vcfs. The SBS VCFs must not contain DBSs, indels, or other types of mutations.

Usage

VCFsToSBSCatalogs(list.of.SBS.vcfs, ref.genome, trans.ranges = NULL,
  region = "unknown")

Arguments

list.of.SBS.vcfs

List of in-memory data frames of pure SBS mutations -- no DBS or 3+BS mutations. The list names will be the sample ids in the output catalog.

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, 1536: catSBS96 catSBS192 catSBS1536. If trans.ranges = NULL, SBS 192 catalog will not be generated. Each catalog has attributes added. See as.catalog for more details.

Examples

# NOT RUN {
file <- c(system.file("extdata",
                      "Mutect.GRCh37.vcf",
                      package = "ICAMS"))
list.of.SBS.vcfs <- ReadAndSplitMutectVCFs(file)$SBS
catalogs.SBS <- VCFsToSBSCatalogs(list.of.SBS.vcfs, ref.genome = "hg19",
                                  trans.ranges = trans.ranges.GRCh37,
                                  region = "genome")
# }

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