get_mut_type {MutationalPatterns} | R Documentation |
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.
get_mut_type(vcf_list, type = c("snv", "indel", "dbs", "mbs"))
vcf_list |
GRanges/GRangesList |
type |
The type of variant that will be returned. |
GRanges/GRangesList of the desired mutation type.
## 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")