makeMLS: Make a MethylationLociSet for a type of methylation and a...
In PeteHaitch/cometh: Analyse, manage and visualise co-methylation data.

Description Usage Arguments Value Note

Construct an object to store the location of all methylation loci of the given type in a genome sequence. For example, find all CpGs in the human reference genome (hg19). The returned object is a MethylationLociSet.

1	makeMLS(methylation_type, bsgenome)

`methylation_type`	A character. The possible values are "CG", "CHG", "CHH" or "CNN" or multiple values specified as a character vector, e.g. c("CG", "CHG") or c("CHG", "CG") for "CG/CHG" methylation.
`bsgenome`	A `BSgenome` object of the reference genome.
`...`	Other arguments passed to `[Biostrings]matchPattern`.

A MethylationLociSet object.

This is basically a wrapper around the [Biostrings]matchPattern function, where methylation_type = pattern and bsgenome = subject. WARNING: This will use a considerable amount of memory and take some time for non-CG methylation.