StrelkaSBSVCFFilesToCatalogAndPlotToPdf | R Documentation |
Create 3 SBS catalogs (96, 192, 1536) and 3 DBS catalogs (78, 136, 144) from
the Strelka SBS VCFs specified by files
and plot them to PDF. 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.
StrelkaSBSVCFFilesToCatalogAndPlotToPdf(
files,
ref.genome,
trans.ranges = NULL,
region = "unknown",
names.of.VCFs = NULL,
output.file = "",
return.annotated.vcfs = FALSE,
suppress.discarded.variants.warnings = TRUE
)
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 |
output.file |
Optional. The base name of the PDF files to be produced;
multiple files will be generated, each ending 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. |
This function calls StrelkaSBSVCFFilesToCatalog
and
PlotCatalogToPdf
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 column
discarded.reason
for more details.
annotated.vcfs
:
Non-NULL only if return.annotated.vcfs
= TRUE.
A list of elements:
SBS
: SBS VCF annotated by AnnotateSBSVCF
with
three new columns SBS96.class
, SBS192.class
and
SBS1536.class
showing the mutation class for each SBS variant.
DBS
: DBS VCF annotated by AnnotateDBSVCF
with
three new columns DBS78.class
, DBS136.class
and
DBS144.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.
SBS 192 and DBS 144 catalogs include only mutations in transcribed regions.
To add or change attributes of the catalog, you can use function
attr
.
For example, attr(catalog, "abundance")
<- custom.abundance
.
file <- c(system.file("extdata/Strelka-SBS-vcf",
"Strelka.SBS.GRCh37.s1.vcf",
package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
catalogs <-
StrelkaSBSVCFFilesToCatalogAndPlotToPdf(file, ref.genome = "hg19",
trans.ranges = trans.ranges.GRCh37,
region = "genome",
output.file =
file.path(tempdir(), "StrelkaSBS"))}
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