R: Get variants with mut_type from GRanges

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.

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")