align-utils            package: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 'PairwiseAlignedFixedSubject':
       coverage(x, shift=0L, width=NULL, weight=1L)
       compareStrings(pattern, subject)

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

Arguments:

       x: A 'character' vector or matrix, 'XStringSet', 'XStringViews',
          'PairwiseAlignedXStringSet', 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', 'PairwiseAlignedXStringSet'. If 'pattern' is a
          'PairwiseAlignedXStringSet' object, then 'subject' must be
          missing. 

 as.prob: If 'TRUE' then probabilities are reported, otherwise counts
          (the default). 

    freq: This argument is deprecated. Please use the 'as.prob'
          argument instead. 

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
     'PairwiseAlignedXStringSet' object.

     'mismatchSummary':  a list of data.frame objects containing counts
     and frequencies of the mismatches for the 'AlignedXStringSet' or
     'PairwiseAlignedFixedSubject' 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,
     PairwiseAlignedXStringSet-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]

