getMethContext: Get Methylation Context from a chromosome DNA sequence

In genomaths/MethylIT.utils: MethylIT utility

Get Methylation Context from a chromosome DNA sequence

Description

This function retrieves the methylation context from a chromosome DNA sequence in fasta format.

Usage

getMethContext(chr.seq, chromosome, verbose = TRUE)

Arguments

chr.seq	DNA sequence from a chromosome in fasta format.
chromosome	Chromosome name.
verbose	If TRUE, prints the function log to stdout

Value

GRanges object with three columns: 'trinucleotide', methylation context, and 'CHH' methylation subcontexts: 'CHA', 'CHC', and 'CHT'.

Examples

dna <- Biostrings::DNAString(x = 'CCCTAACGACCCTAACGCTACCCTAAACCTCTGAAT',
    start = 1, nchar = NA)
getMethContext(chr.seq = dna, chromosome = '1', verbose = TRUE)

genomaths/MethylIT.utils documentation built on July 4, 2023, 12:05 a.m.