findLoci: Find methylation loci in a genome
In bsseq: Analyze, manage and store bisulfite sequencing data

Description Usage Arguments Details Value Author(s) See Also Examples

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().

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

`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.

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.

A GRanges object storing the found loci.

Peter F. Hickey

Biostrings::vmatchPattern()
?BSgenome::`BSgenome-utils`

  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 = "+")
  }