View source: R/VCF_to_catalog_functions.R
ReadVCFs | R Documentation |
Read VCF files
ReadVCFs(
files,
variant.caller = "unknown",
num.of.cores = 1,
names.of.VCFs = NULL,
tumor.col.names = NA,
filter.status = DefaultFilterStatus(variant.caller),
get.vaf.function = NULL,
...
)
files |
Character vector of file paths to the VCF files. |
variant.caller |
Name of the variant caller that produces the VCF, can
be either |
num.of.cores |
The number of cores to use. Not available on Windows
unless |
names.of.VCFs |
Optional. Character vector of names of the VCF files.
The order of names in |
tumor.col.names |
Optional. Only applicable to Mutect VCFs.
Vector of column names or column indices in Mutect VCFs which
contain the tumor sample information. The order of elements in
|
filter.status |
The character string in column |
get.vaf.function |
Optional. Only applicable when |
... |
Optional arguments to |
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.
file <- c(system.file("extdata/Mutect-vcf",
"Mutect.GRCh37.s1.vcf",
package = "ICAMS"))
list.of.vcfs <- ReadVCFs(file, variant.caller = "mutect")
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