Read VCF files
ReadVCFs(
files,
variant.caller = NULL,
names.of.VCFs = NULL,
tumor.col.names = NA
)Character vector of file paths to the VCF files.
Name of the variant caller that produces all
the VCFs specified by files, can be either strelka,
mutect or freebayes. This information is needed to calculate
the VAFs (variant allele frequencies). If NULL(default), then VAF and
read depth information will not be added to the original VCFs.
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) and file
paths without extensions (and the leading dot) will be used as the names of
the VCF files.
Optional. Only applicable to Mutect VCFs.
Character vector of column names in Mutect VCFs which contain the
tumor sample information. The order of names in tumor.col.names
should match the order of Mutect VCFs specified in files.
If tumor.col.names is equal to NA(default), this function
will use the 10th column in all the Mutect VCFs to calculate VAFs.
See GetMutectVAF for more details.
A list of data frames storing data lines of the VCF files with two additional columns added which contain the VAF(variant allele frequency) and read depth information.