mutation_context: This function has been removed. Use 'mut_context' instead.

Description Usage Arguments Value See Also Examples

View source: R/mut_context.R

Description

This function has been removed. Use 'mut_context' instead.

Usage

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mutation_context(vcf, ref_genome)

Arguments

vcf

A GRanges object

ref_genome

The reference genome

Value

Character vector with the context of the base substitutions

See Also

mut_context

Examples

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## 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)

MutationalPatterns documentation built on Nov. 17, 2017, 11:10 a.m.