ReadAndSplitStrelkaSBSVCFs {ICAMS} | R Documentation |
Read and split Strelka SBS VCF files
Description
The function will find and merge adjacent SBS pairs into DBS if their VAFs are very similar. The default threshold value for VAF is 0.02.
Usage
ReadAndSplitStrelkaSBSVCFs(
files,
names.of.VCFs = NULL,
suppress.discarded.variants.warnings = TRUE
)
Arguments
files |
Character vector of file paths to the Strelka SBS VCF files. |
names.of.VCFs |
Optional. Character vector of names of the VCF files.
The order of names in |
suppress.discarded.variants.warnings |
Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE. |
Value
A list of elements as follows:
-
SBS.vcfs
: List of data.frames of pure SBS mutations – no DBS or 3+BS mutations. -
DBS.vcfs
: List of data.frames of pure DBS mutations – no SBS or 3+BS mutations. -
discarded.variants
: Non-NULL only if there are variants that were excluded from the analysis. See the added extra columndiscarded.reason
for more details.
See Also
Examples
file <- c(system.file("extdata/Strelka-SBS-vcf",
"Strelka.SBS.GRCh37.s1.vcf",
package = "ICAMS"))
list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs(file)