maftools (version 0.99.30)

trinucleotideMatrix: Extract single 5' and 3' bases flanking the mutated site.

Description

Extract single 5' and 3' bases flanking the mutated site.

Usage

trinucleotideMatrix(maf, ref_genome, prefix = NULL, add = TRUE,
  ignoreChr = NULL, useSyn = FALSE)

Arguments

maf

an MAF object generated by read.maf

ref_genome

faidx indexed refrence fasta file.

prefix

Prefix to add or remove from contig names in MAF file.

add

If prefix is used, default is to add prefix to contig names in MAF file. If false prefix will be removed from contig names.

ignoreChr

Chromsomes to remove from analysis. e.g. chrM

useSyn

Logical. Whether to include synonymous variants in analysis. Defaults to FALSE.

Value

A matrix of dimension nx96, where n is the number of samples in the MAF.

Details

Extracts immediate 5' and 3' bases flanking the mutated site and classifies them into 96 substitution classes. This function loads reference genome into memeory. Typical human geneome occupies a peak memory of ~3 gb while extracting bases.

See Also

extractSignatures

Examples

# NOT RUN {
laml.tnm <- trinucleotideMatrix(maf = laml, ref_genome = 'hg19.fa',
prefix = 'chr', add = TRUE, useSyn = TRUE)
# }
# NOT RUN {
# }