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 column
discarded.reason for more details.
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 names.of.VCFs should match the order of VCF
file paths in files. If NULL(default), this function will
remove all of the path up to and including the last path separator (if any)
in files and file paths without extensions (and the leading dot)
will be used as the names of the VCF files.
suppress.discarded.variants.warnings
Logical. Whether to suppress
warning messages showing information about the discarded variants. Default
is TRUE.