get_mut_type: Get variants with mut_type from GRanges

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

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"),
  predefined_dbs_mbs = FALSE
)

Arguments

vcf_list	GRanges/GRangesList
type	The type of variant that will be returned.
predefined_dbs_mbs	Boolean. Whether dbs and mbs variants have been predefined in your vcf. This function by default assumes that dbs and mbs variants are present in the vcf as snvs, which are positioned next to each other. If your dbs/mbs variants are called separately you should set this argument to TRUE. (default = FALSE)

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"
))

## Here we only use two samples to reduce runtime
grl <- grl[1:2]

## 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")

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.