BSgenome-utils {BSgenome} | R Documentation

## BSgenome utilities

### Description

Utilities for BSgenome objects.

### Usage

    ## S4 method for signature 'BSgenome'
    matchPWM(pwm, subject, min.score = "80%", exclude = "",
           maskList = logical(0))
    ## S4 method for signature 'BSgenome'
    countPWM(pwm, subject, min.score = "80%", exclude = "",
           maskList = logical(0))
    ## S4 method for signature 'BSgenome'
    vmatchPattern(pattern, subject, max.mismatch = 0, min.mismatch = 0,
                with.indels = FALSE, fixed = TRUE, algorithm = "auto",
                exclude = "", maskList = logical(0),  userMask =
                   IRangesList(), invertUserMask = FALSE)
    ## S4 method for signature 'BSgenome'
    vcountPattern(pattern, subject, max.mismatch = 0, min.mismatch = 0,
                with.indels = FALSE, fixed = TRUE, algorithm = "auto",
                exclude = "", maskList = logical(0),  userMask =
                   IRangesList(), invertUserMask = FALSE)
    ## S4 method for signature 'BSgenome'
    vmatchPDict(pdict, subject, max.mismatch = 0, min.mismatch = 0,
              fixed = TRUE, algorithm = "auto", verbose = FALSE,
              exclude = "", maskList = logical(0))
    ## S4 method for signature 'BSgenome'
    vcountPDict(pdict, subject, max.mismatch = 0, min.mismatch = 0,
              fixed = TRUE, algorithm = "auto", collapse = FALSE,
              weight = 1L, verbose = FALSE, exclude = "", maskList = logical(0))

### Arguments

`pwm` | A numeric matrix with row names A, C, G and T representing a Position Weight Matrix.
`pattern` | A DNAString object containing the pattern sequence.
`pdict` | A DNAStringSet object containing the pattern sequences.
`subject` | A BSgenome object containing the subject sequences.
`min.score` | The minimum score for counting a match. Can be given as a character string containing a percentage (e.g. `"85%"`) of the highest possible score or as a single number.
`max.mismatch, min.mismatch` | The maximum and minimum number of mismatching letters allowed (see `?`lowlevel-matching`` for the details). If non-zero, an inexact matching algorithm is used.
`with.indels` | If `TRUE` then indels are allowed. In that case, `min.mismatch` must be `0` and `max.mismatch` is interpreted as the maximum "edit distance" allowed between any pattern and any of its matches (see `?`matchPattern`` for the details).
`fixed` | If `FALSE` then IUPAC extended letters are interpreted as ambiguities (see `?`lowlevel-matching`` for the details).
`algorithm` | For `vmatchPattern` and `vcountPattern` one of the following: `"auto"`, `"naive-exact"`, `"naive-inexact"`, `"boyer-moore"`, `"shift-or"`, or `"indels"`. For `vmatchPDict` and `vcountPDict` one of the following: `"auto"`, `"naive-exact"`, `"naive-inexact"`, `"boyer-moore"`, or `"shift-or"`.
`collapse, weight` | ignored arguments.
`verbose` | `TRUE` or `FALSE`.
`exclude` | A character vector with strings that will be used to filter out chromosomes whose names match these strings.
`maskList` | A named logical vector of maskStates preferred when used with a BSGenome object. When using the bsapply function, the masks will be set to the states in this vector.
`userMask` | An IntegerRangesList, containing a mask to be applied to each chromosome. See `bsapply`.
`invertUserMask` | Whether the `userMask` should be inverted.

### Value

A GRanges object for `matchPWM` with two elementMetadata columns: "score" (numeric), and "string" (DNAStringSet).

A GRanges object for `vmatchPattern`.

A GRanges object for `vmatchPDict` with one elementMetadata column: "index", which represents a mapping to a position in the original pattern dictionary.

A data.frame object for `countPWM` and `vcountPattern` with three columns: "seqname" (factor), "strand" (factor), and "count" (integer).

A DataFrame object for `vcountPDict` with four columns: "seqname" ('factor' Rle), "strand" ('factor' Rle), "index" (integer) and "count" ('integer' Rle). As with `vmatchPDict` the index column represents a mapping to a position in the original pattern dictionary.

### Author(s)

P. Aboyoun

### See Also

`matchPWM`, `matchPattern`, `matchPDict`, `bsapply`

### Examples

      library(BSgenome.Celegans.UCSC.ce2)
      data(HNF4alpha)

      pwm <- PWM(HNF4alpha)
      matchPWM(pwm, Celegans)
      countPWM(pwm, Celegans)

      pattern <- consensusString(HNF4alpha)
      vmatchPattern(pattern, Celegans, fixed = "subject")
      vcountPattern(pattern, Celegans, fixed = "subject")

      vmatchPDict(HNF4alpha[1:10], Celegans)
      vcountPDict(HNF4alpha[1:10], Celegans)

[Package BSgenome version 1.52.0 Index]