mut_type_occurrences {MutationalPatterns} | R Documentation |
Count the occurrences of each base substitution type
mut_type_occurrences(vcf_list, ref_genome)
vcf_list |
GRangesList or GRanges object. |
ref_genome |
BSgenome reference genome object |
data.frame with counts of each base substitution type for each sample in vcf_list
## See the 'read_vcfs_as_granges()' example for how we obtained the ## following data: vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds", package = "MutationalPatterns" )) ## Load a reference genome. ref_genome <- "BSgenome.Hsapiens.UCSC.hg19" library(ref_genome, character.only = TRUE) ## Get the type occurrences for all VCF objects. type_occurrences <- mut_type_occurrences(vcfs, ref_genome)