Read Mutect VCF files.
ReadMutectVCFs(files, names.of.VCFs = NULL, tumor.col.names = NA)
A list of data frames which store data lines of VCF files with two additional columns added which contain the VAF(variant allele frequency) and read depth information.
Character vector of file paths to the VCF files.
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.
Character vector of column names in VCFs which contain
the tumor sample information. The order of names in tumor.col.names
should match the order of VCFs specified in files
. If
tumor.col.names
is equal to NA
(default), this function will
use the 10th column in all the VCFs to calculate VAFs.
See GetMutectVAF
for more details.