match-utils {Biostrings} | R Documentation

## Utility functions operating on the matches returned by a high-level matching function

### Description

Miscellaneous utility functions operating on the matches returned by a high-level matching function like `matchPattern`, `matchPDict`, etc...

### Usage

    mismatch(pattern, x, fixed=TRUE)
    nmatch(pattern, x, fixed=TRUE)
    nmismatch(pattern, x, fixed=TRUE)
    ## S4 method for signature 'MIndex'
    coverage(x, shift=0L, width=NULL, weight=1L)
    ## S4 method for signature 'MaskedXString'
    coverage(x, shift=0L, width=NULL, weight=1L)

### Arguments

`pattern` | The pattern string.
`x` | An XStringViews object for `mismatch` (typically, one returned by `matchPattern(pattern, subject)`). An MIndex object for `coverage`, or any object for which a `coverage` method is defined. See `?coverage`.
`fixed` | See `?`lowlevel-matching``.
`shift, width` | See `?coverage`.
`weight` | An integer vector specifying how much each element in `x` counts.

### Details

The `mismatch` function gives the positions of the mismatching letters of a given pattern relatively to its matches in a given subject.

The `nmatch` and `nmismatch` functions give the number of matching and mismatching letters produced by the `mismatch` function.

The `coverage` function computes the "coverage" of a subject by a given pattern or set of patterns.

### Value

`mismatch`: a list of integer vectors.

`nmismatch`: an integer vector containing the length of the vectors produced by `mismatch`.

`coverage`: an Rle object indicating the coverage of `x`. See `?coverage` for the details. If `x` is an MIndex object, the coverage of a given position in the underlying sequence (typically the subject used during the search that returned `x`) is the number of matches (or hits) it belongs to.

### See Also

lowlevel-matching, `matchPattern`, `matchPDict`, XString-class, XStringViews-class, MIndex-class, coverage, align-utils

### Examples

      ## ---------------------------------------------------------------------
      ## mismatch() / nmismatch()
      ## ---------------------------------------------------------------------
      subject <- DNAString("ACGTGCA")
      m <- matchPattern("NCA", subject, max.mismatch=1, fixed=FALSE)
      mismatch("NCA", m)
      nmismatch("NCA", m)

      ## ---------------------------------------------------------------------
      ## coverage()
      ## ---------------------------------------------------------------------
      coverage(m)

      ## See ?matchPDict for examples of using coverage() on an MIndex object...

[Package Biostrings version 2.56.0 Index]