StrelkaSBSVCFFilesToCatalog {ICAMS} | R Documentation |
Create SBS and DBS catalogs from Strelka SBS VCF files
Description
Create 3 SBS catalogs (96, 192, 1536) and 3 DBS catalogs (78, 136, 144) from
the Strelka SBS VCFs specified by files
. 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
StrelkaSBSVCFFilesToCatalog(
files,
ref.genome,
trans.ranges = NULL,
region = "unknown",
names.of.VCFs = NULL,
return.annotated.vcfs = FALSE,
suppress.discarded.variants.warnings = TRUE
)
Arguments
files |
Character vector of file paths to the Strelka SBS VCF files. |
ref.genome |
A |
trans.ranges |
Optional. If
then the function will infer |
region |
A character string designating a genomic region;
see |
names.of.VCFs |
Optional. Character vector of names of the VCF files.
The order of names in |
return.annotated.vcfs |
Logical. Whether to return the annotated VCFs with additional columns showing mutation class for each variant. Default is FALSE. |
suppress.discarded.variants.warnings |
Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE. |
Details
This function calls VCFsToSBSCatalogs
and
VCFsToDBSCatalogs
.
Value
A list containing the following objects:
-
catSBS96
,catSBS192
,catSBS1536
: Matrix of 3 SBS catalogs (one each for 96, 192, and 1536). -
catDBS78
,catDBS136
,catDBS144
: Matrix of 3 DBS catalogs (one each for 78, 136, and 144). -
discarded.variants
: Non-NULL only if there are variants that were excluded from the analysis. See the added extra columndiscarded.reason
for more details. -
annotated.vcfs
: Non-NULL only ifreturn.annotated.vcfs
= TRUE. A list of elements:-
SBS
: SBS VCF annotated byAnnotateSBSVCF
with three new columnsSBS96.class
,SBS192.class
andSBS1536.class
showing the mutation class for each SBS variant. -
DBS
: DBS VCF annotated byAnnotateDBSVCF
with three new columnsDBS78.class
,DBS136.class
andDBS144.class
showing the mutation class for each DBS variant.
-
If trans.ranges
is not provided by user and cannot be inferred by
ICAMS, SBS 192 and DBS 144 catalog will not be generated. Each catalog has
attributes added. See as.catalog
for more details.
Note
SBS 192 and DBS 144 catalogs include only mutations in transcribed regions.
Comments
To add or change attributes of the catalog, you can use function
attr
.
For example, attr(catalog, "abundance")
<- custom.abundance
.
Examples
file <- c(system.file("extdata/Strelka-SBS-vcf",
"Strelka.SBS.GRCh37.s1.vcf",
package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
catalogs <- StrelkaSBSVCFFilesToCatalog(file, ref.genome = "hg19",
trans.ranges = trans.ranges.GRCh37,
region = "genome")}