findLoci {bsseq} | R Documentation

## Find methylation loci in a genome

### Description

This is a convenience function to find methylation loci, such as CpGs, in a reference genome. The result is useful as the value of the `loci` argument for `read.bismark()`.

### Usage

    findLoci(pattern,
             subject,
             include = seqlevels(subject),
             strand = c("*", "+", "-"),
             fixed = "subject",
             resize = TRUE)

### Arguments

`pattern` | A string specifying the pattern to search for, e.g. `"CG"`. Can contain IUPAC ambiguity codes, e.g., `"CH"`.
`subject` | A string containing a file path to the genome sequence, in FASTA or 2bit format, to be searched. Alternatively, a BSgenome or DNAStringSet object storing the genome sequence to be searched.
`include` | A character vector indicating the seqlevels of `subject` to be used.
`strand` | A character scaler specifying the strand of `subject` to be used. If `strand = "*"`, then both the positive (`strand = "+"`) and negative (`strand = "-"` strands will be searched.) It is assumed that `subject` contains the sequence with respect to the `+` strand.
`fixed` | If `"subject"` (the default), IUPAC ambiguity codes in the pattern only are interpreted as wildcards, e.g., a `pattern` containing `CH` matches a `subject` containing `CA` but not vice versa. See `?Biostrings::`lowlevel-matching`` for more information
`resize` | A logical scalar specifying whether the ranges should be shifted to have width 1 and anchored by the start of the locus, e.g., resize a CpG dinucleotide to give the co-ordinates of the cytosine.

### Details

This function provides a convenience wrapper for finding methylation loci in a genome, based on running `vmatchPattern()`. Users requiring finer-grained control should directly use the `vmatchPattern()` function and coerce the result to a GRanges object.

### Value

A GRanges object storing the found loci.

### Author(s)

Peter F. Hickey

### See Also

- `Biostrings::vmatchPattern()`

- `?BSgenome::`BSgenome-utils``

### Examples

      library(Biostrings)
      # Find CpG dinucleotides on the both strands of an artificial sequence
      my_seq <- DNAStringSet("ATCAGTCGC")
      names(my_seq) <- "test"
      findLoci(pattern = "CG", subject = my_seq)
      # Find CHG trinucleotides on the both strands of an artificial sequence
      findLoci(pattern = "CHG", subject = my_seq)

      # Find CpG dinucleotides on the + strand of chr17 from the human genome (hg38)
      if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
        findLoci(
            pattern = "CG",
            subject = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
            include = "chr17",
            strand = "+")
      }

[Package bsseq version 1.26.0 Index]