ICAMS (version 2.0.7)

VCFsToDBSCatalogs: Create DBS catalogs from VCFs

Description

Create a list of 3 catalogs (one each for DBS78, DBS144 and DBS136) out of the contents in list.of.DBS.vcfs. The VCFs must not contain any type of mutation other then DBSs.

Usage

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

Arguments

list.of.DBS.vcfs

List of in-memory data frames of pure DBS mutations -- no SBS 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 DBS catalogs, one each for 78, 144, 136: catDBS78 catDBS144 catDBS136. If trans.ranges = NULL, DBS 144 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.DBS.vcfs <- ReadAndSplitMutectVCFs(file)$DBS
catalogs.DBS <- VCFsToDBSCatalogs(list.of.DBS.vcfs, ref.genome = "hg19",
                                  trans.ranges = trans.ranges.GRCh37,
                                  region = "genome")
# }