align-utils {Biostrings} | R Documentation

## Utility functions related to sequence alignment

### Description

A variety of different functions used to deal with sequence alignments.

### Usage

    nedit(x) # also nmatch and nmismatch

    mismatchTable(x, shiftLeft=0L, shiftRight=0L, ...)
    mismatchSummary(x, ...)
    ## S4 method for signature 'AlignedXStringSet0'
    coverage(x, shift=0L, width=NULL, weight=1L)
    ## S4 method for signature 'PairwiseAlignmentsSingleSubject'
    coverage(x, shift=0L, width=NULL, weight=1L)
    compareStrings(pattern, subject)

    ## S4 method for signature 'PairwiseAlignmentsSingleSubject'
    consensusMatrix(x,
                    as.prob=FALSE, shift=0L, width=NULL,
                    baseOnly=FALSE, gapCode="-", endgapCode="-")

### Arguments

`x` | A `character` vector or matrix, `XStringSet`, `XStringViews`, `PairwiseAlignments`, or `list` of FASTA records containing the equal-length strings.
`shiftLeft, shiftRight` | Non-positive and non-negative integers respectively that specify how many preceding and succeeding characters to and from the mismatch position to include in the mismatch substrings.
`...` | Further arguments to be passed to or from other methods.
`shift, width` | See `?coverage`.
`weight` | An integer vector specifying how much each element in `x` counts.
`pattern, subject` | The strings to compare. Can be of type `character`, `XString`, `XStringSet`, `AlignedXStringSet`, or, in the case of `pattern`, `PairwiseAlignments`. If `pattern` is a `PairwiseAlignments` object, then `subject` must be missing.
`as.prob` | If `TRUE` then probabilities are reported, otherwise counts (the default).
`baseOnly` | `TRUE` or `FALSE`. If `TRUE`, the returned vector only contains frequencies for the letters in the "base" alphabet i.e. "A", "C", "G", "T" if `x` is a "DNA input", and "A", "C", "G", "U" if `x` is "RNA input". When `x` is a BString object (or an XStringViews object with a BString subject, or a BStringSet object), then the `baseOnly` argument is ignored.
`gapCode, endgapCode` | The codes in the appropriate `alphabet` to use for the internal and end gaps.

### Details

`mismatchTable`: a data.frame containing the positions and substrings of the mismatches for the `AlignedXStringSet` or `PairwiseAlignments` object.

`mismatchSummary`: a list of data.frame objects containing counts and frequencies of the mismatches for the `AlignedXStringSet` or `PairwiseAlignmentsSingleSubject` object.

`compareStrings` combines two equal-length strings that are assumed to be aligned into a single character string containing that replaces mismatches with `"?"`, insertions with `"+"`, and deletions with `"-"`.

### See Also

`pairwiseAlignment`, `consensusMatrix`, XString-class, XStringSet-class, XStringViews-class, AlignedXStringSet-class, PairwiseAlignments-class, match-utils

### Examples

      ## Compare two globally aligned strings
      string1 <- "ACTTCACCAGCTCCCTGGCGGTAAGTTGATC---AAAGG---AAACGCAAAGTTTTCAAG"
      string2 <- "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC"
      compareStrings(string1, string2)

      ## Create a consensus matrix
      nw1 <-
        pairwiseAlignment(AAStringSet(c("HLDNLKGTF", "HVDDMPNAL")), AAString("SMDDTEKMSMKL"),
          substitutionMatrix = "BLOSUM50", gapOpening = 3, gapExtension = 1)
      consensusMatrix(nw1)

      ## Examine the consensus between the bacteriophage phi X174 genomes
      data(phiX174Phage)
      phageConsmat <- consensusMatrix(phiX174Phage, baseOnly = TRUE)
      phageDiffs <- which(apply(phageConsmat, 2, max) < length(phiX174Phage))
      phageDiffs
      phageConsmat[,phageDiffs]

[Package Biostrings version 2.60.2 Index]