read_vcfs_as_granges {MutationalPatterns} | R Documentation

## Read VCF files into a GRangesList

### Description

This function reads Variant Call Format (VCF) files into a GRanges object and combines them in a GRangesList. In addition to loading the files, this function applies the same seqlevel style to the GRanges objects as the reference genome passed in the 'genome' parameter.

### Usage

    read_vcfs_as_granges(vcf_files, sample_names, genome, group = "auto+sex",
      check_alleles = TRUE)

### Arguments

`vcf_files` | Character vector of VCF file names
`sample_names` | Character vector of sample names
`genome` | A string matching the name of a BSgenome library corresponding to the reference genome of your VCFs
`group` | Selector for a seqlevel group. All seqlevels outside of this group will be removed. Possible values: * 'all' for all chromosomes; * 'auto' for autosomal chromosomes; * 'sex' for sex chromosomes; * 'auto+sex' for autosomal + sex chromosomes (default); * 'circular' for circular chromosomes; * 'none' for no filtering, which results in keeping all seqlevels from the VCF file.
`check_alleles` | logical. If TRUE (default) positions with insertions, deletions and/or multiple alternative alleles are excluded from the vcf object, since these positions cannot be analysed with this package. This setting can be set to FALSE to speed up processing time only if the input vcf does not contain any of such positions, as these will cause obscure errors.

### Value

A GRangesList containing the GRanges obtained from 'vcf_files'

### Examples

    # The example data set consists of three colon samples, three intestine
    # samples and three liver samples.  So, to map each file to its appropriate
    # sample name, we create a vector containing the sample names:
    sample_names <- c ( "colon1", "colon2", "colon3",
                        "intestine1", "intestine2", "intestine3",
                        "liver1", "liver2", "liver3" )

    # We assemble a list of files we want to load.  These files match the
    # sample names defined above.
    vcf_files <- list.files(system.file("extdata",
                                        package="MutationalPatterns"),
                                        pattern = ".vcf", full.names = TRUE)

    # Get a reference genome BSgenome object.
    ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
    library("BSgenome")
    library(ref_genome, character.only = TRUE)

    # This function loads the files as GRanges objects
    vcfs <- read_vcfs_as_granges(vcf_files, sample_names, ref_genome)

[Package MutationalPatterns version 1.99.3 Index]