readVcfDir: Reads directory of VCF files

In olivmrtn/MachineLearningGWAS: Machine Learning for Genome Wide Association Studies

Description

Real all Variant Call Format (VCF) files contained in a directory using the VariantAnnotation Bioconductor package.

Usage

readVcfDir(dir, param_function = function(fn)
  VariantAnnotation::ScanVcfParam(), grep_out, n_files, verbose = TRUE, ...)

Arguments

dir	Directory containing VCF files.
param_function	Function to be evaluated and as param argument. Only takes as argument filename and must return a ScanVcfParam object.
grep_out	Regular expression for file names to be filter out.
n_files	If specified, will only import the first n_files in the directory.
verbose	logical specifying if function should be run in verbose mode.
...	Further arguments to pass on to readVcf

Details

Uses list.files to identify files ending with ".vcf"'.

Value

A list of VCF objects.

See Also

readVcf

olivmrtn/MachineLearningGWAS documentation built on May 24, 2019, 12:52 p.m.