mut_matrix {MutationalPatterns} | R Documentation |
Make 96 trinucleotide mutation count matrix
mut_matrix(vcf_list, ref_genome)
vcf_list |
List of collapsed vcf objects |
ref_genome |
BSGenome reference genome object |
96 mutation count matrix
## 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 the corresponding reference genome. ref_genome = "BSgenome.Hsapiens.UCSC.hg19" library(ref_genome, character.only = TRUE) ## Construct a mutation matrix from the loaded VCFs in comparison to the ## ref_genome. mut_mat <- mut_matrix(vcf_list = vcfs, ref_genome = ref_genome)