get_mut_type {MutationalPatterns} | R Documentation

## Get variants with mut_type from GRanges

### Description

Get the variants of a certain mutation type from a GRanges or GRangesList object. All other variants will be filtered out. It is assumed that DBS/MBSs are called as separate SNVs. They are merged into single variants. The type of variant can be chosen with type.

### Usage

    get_mut_type(vcf_list, type = c("snv", "indel", "dbs", "mbs"))

### Arguments

`vcf_list` | GRanges/GRangesList
`type` | The type of variant that will be returned.

### Value

GRanges/GRangesList of the desired mutation type.

### See Also

`read_vcfs_as_granges`

### Examples

    ## Get a GRanges list object.
    ## See 'read_vcfs_as_granges' for more info how to do this.
    grl <- readRDS(system.file("states/blood_grl.rds",
      package = "MutationalPatterns"
    ))

    ## Get a specific mutation type.
    snv_grl <- get_mut_type(grl, "snv")
    indel_grl <- get_mut_type(grl, "indel")
    dbs_grl <- get_mut_type(grl, "dbs")
    mbs_grl <- get_mut_type(grl, "mbs")

[Package MutationalPatterns version 3.0.1 Index]