R: Get Methylation Context from a chromosome DNA sequence

R Documentation

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)

[Package MethylIT.utils version 0.3.1 ]