mutation_context {MutationalPatterns} | R Documentation |
This function has been removed. Use 'mut_context' instead.
mutation_context(vcf, ref_genome)
vcf |
A GRanges object |
ref_genome |
The reference genome |
Character vector with the context of the base substitutions
## 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) mut_context <- mut_context(vcfs[[1]], ref_genome)