lowlevel-matching {Biostrings} | R Documentation

## Low-level matching functions

### Description

In this man page we define precisely and illustrate what a "match" of a pattern P in a subject S is in the context of the Biostrings package. This definition of a "match" is central to most pattern matching functions available in this package: unless specified otherwise, most of them will adhere to the definition provided here.

`hasLetterAt` checks whether a sequence or set of sequences has the specified letters at the specified positions.

`neditAt`, `isMatchingAt` and `which.isMatchingAt` are low-level matching functions that only look for matches at the specified positions in the subject.

### Usage

    hasLetterAt(x, letter, at, fixed=TRUE)

    ## neditAt() and related utils:
    neditAt(pattern, subject, at=1,
            with.indels=FALSE, fixed=TRUE)
    neditStartingAt(pattern, subject, starting.at=1,
            with.indels=FALSE, fixed=TRUE)
    neditEndingAt(pattern, subject, ending.at=1,
            with.indels=FALSE, fixed=TRUE)

    ## isMatchingAt() and related utils:
    isMatchingAt(pattern, subject, at=1,
            max.mismatch=0, min.mismatch=0, with.indels=FALSE, fixed=TRUE)
    isMatchingStartingAt(pattern, subject, starting.at=1,
            max.mismatch=0, min.mismatch=0, with.indels=FALSE, fixed=TRUE)
    isMatchingEndingAt(pattern, subject, ending.at=1,
            max.mismatch=0, min.mismatch=0, with.indels=FALSE, fixed=TRUE)

    ## which.isMatchingAt() and related utils:
    which.isMatchingAt(pattern, subject, at=1,
            max.mismatch=0, min.mismatch=0, with.indels=FALSE, fixed=TRUE,
            follow.index=FALSE, auto.reduce.pattern=FALSE)
    which.isMatchingStartingAt(pattern, subject, starting.at=1,
            max.mismatch=0, min.mismatch=0, with.indels=FALSE, fixed=TRUE,
            follow.index=FALSE, auto.reduce.pattern=FALSE)
    which.isMatchingEndingAt(pattern, subject, ending.at=1,
            max.mismatch=0, min.mismatch=0, with.indels=FALSE, fixed=TRUE,
            follow.index=FALSE, auto.reduce.pattern=FALSE)

### Arguments

`x` | A character vector, or an XString or XStringSet object.
`letter` | A character string or an XString object containing the letters to check.
`at, starting.at, ending.at` | An integer vector specifying the starting (for `starting.at` and `at`) or ending (for `ending.at`) positions of the pattern relatively to the subject. With `auto.reduce.pattern` (below), either a single integer or a constant vector of length `nchar(pattern)` (below), to which the former is immediately converted. For the `hasLetterAt` function, `letter` and `at` must have the same length.
`pattern` | The pattern string (but see `auto.reduce.pattern`, below).
`subject` | A character vector, or an XString or XStringSet object containing the subject sequence(s).
`max.mismatch, min.mismatch` | Integer vectors of length >= 1 recycled to the length of the `at` (or `starting.at`, or `ending.at`) argument. More details below.
`with.indels` | See details below.
`fixed` | Only with a DNAString or RNAString-based subject can a `fixed` value other than the default (`TRUE`) be used. If `TRUE` (the default), an IUPAC ambiguity code in the pattern can only match the same code in the subject, and vice versa. If `FALSE`, an IUPAC ambiguity code in the pattern can match any letter in the subject that is associated with the code, and vice versa. See `IUPAC_CODE_MAP` for more information about the IUPAC Extended Genetic Alphabet. `fixed` can also be a character vector, a subset of `c("pattern", "subject")`. `fixed=c("pattern", "subject")` is equivalent to `fixed=TRUE` (the default). An empty vector is equivalent to `fixed=FALSE`. With `fixed="subject"`, ambiguities in the pattern only are interpreted as wildcards. With `fixed="pattern"`, ambiguities in the subject only are interpreted as wildcards.
`follow.index` | Whether the single integer returned by `which.isMatchingAt` (and related utils) should be the first *value* in `at` for which a match occurred, or its *index* in `at` (the default).
`auto.reduce.pattern` | Whether `pattern` should be effectively shortened by 1 letter, from its beginning for `which.isMatchingStartingAt` and from its end for `which.isMatchingEndingAt`, for each successive `(at, max.mismatch)` "pair".

### Details

A "match" of pattern P in subject S is a substring S' of S that is considered similar enough to P according to some distance (or metric) specified by the user. 2 distances are supported by most pattern matching functions in the Biostrings package. The first (and simplest) one is the "number of mismatching letters". It is defined only when the 2 strings to compare have the same length, so when this distance is used, only matches that have the same number of letters as P are considered. The second one is the "edit distance" (aka Levenshtein distance): it's the minimum number of operations needed to transform P into S', where an operation is an insertion, deletion, or substitution of a single letter. When this metric is used, matches can have a different number of letters than P.

The `neditAt` function implements these 2 distances. If `with.indels` is `FALSE` (the default), then the first distance is used i.e. `neditAt` returns the "number of mismatching letters" between the pattern P and the substring S' of S starting at the positions specified in `at` (note that `neditAt` is vectorized so a long vector of integers can be passed thru the `at` argument). If `with.indels` is `TRUE`, then the "edit distance" is used: for each position specified in `at`, P is compared to all the substrings S' of S starting at this position and the smallest distance is returned. Note that this distance is guaranteed to be reached for a substring of length < 2*length(P) so, of course, in practice, P only needs to be compared to a small number of substrings for every starting position.

### Value

`hasLetterAt`: A logical matrix with one row per element in `x` and one column per letter/position to check. When a specified position is invalid with respect to an element in `x` then the corresponding matrix element is set to NA.

`neditAt`: If `subject` is an XString object, then return an integer vector of the same length as `at`. If `subject` is an XStringSet object, then return the integer matrix with `length(at)` rows and `length(subject)` columns defined by:

        sapply(unname(subject),
               function(x) neditAt(pattern, x, ...))

`neditStartingAt` is identical to `neditAt` except that the `at` argument is now called `starting.at`. `neditEndingAt` is similar to `neditAt` except that the `at` argument is now called `ending.at` and must contain the ending positions of the pattern relatively to the subject.

`isMatchingAt`: If `subject` is an XString object, then return the logical vector defined by:

        min.mismatch <= neditAt(...) <= max.mismatch

If `subject` is an XStringSet object, then return the logical matrix with `length(at)` rows and `length(subject)` columns defined by:

        sapply(unname(subject),
               function(x) isMatchingAt(pattern, x, ...))

`isMatchingStartingAt` is identical to `isMatchingAt` except that the `at` argument is now called `starting.at`. `isMatchingEndingAt` is similar to `isMatchingAt` except that the `at` argument is now called `ending.at` and must contain the ending positions of the pattern relatively to the subject.

`which.isMatchingAt`: The default behavior (`follow.index=FALSE`) is as follow. If `subject` is an XString object, then return the single integer defined by:

        which(isMatchingAt(...))[1]

If `subject` is an XStringSet object, then return the integer vector defined by:

        sapply(unname(subject),
               function(x) which.isMatchingAt(pattern, x, ...))

If `follow.index=TRUE`, then the returned value is defined by:

        at[which.isMatchingAt(..., follow.index=FALSE)]

`which.isMatchingStartingAt` is identical to `which.isMatchingAt` except that the `at` argument is now called `starting.at`. `which.isMatchingEndingAt` is similar to `which.isMatchingAt` except that the `at` argument is now called `ending.at` and must contain the ending positions of the pattern relatively to the subject.

### See Also

`nucleotideFrequencyAt`, `matchPattern`, `matchPDict`, `matchLRPatterns`, `trimLRPatterns`, `IUPAC_CODE_MAP`, XString-class, align-utils

### Examples

      ## ---------------------------------------------------------------------
      ## hasLetterAt()
      ## ---------------------------------------------------------------------
      x <- DNAStringSet(c("AAACGT", "AACGT", "ACGT", "TAGGA"))
      hasLetterAt(x, "AAAAAA", 1:6)

      ## hasLetterAt() can be used to answer questions like: "which elements
      ## in 'x' have an A at position 2 and a G at position 4?"
      q1 <- hasLetterAt(x, "AG", c(2, 4))
      which(rowSums(q1) == 2)

      ## or "how many probes in the drosophila2 chip have T, G, T, A at
      ## position 2, 4, 13 and 20, respectively?"
      library(drosophila2probe)
      probes <- DNAStringSet(drosophila2probe)
      q2 <- hasLetterAt(probes, "TGTA", c(2, 4, 13, 20))
      sum(rowSums(q2) == 4)
      ## or "what's the probability to have an A at position 25 if there is
      ## one at position 13?"
      q3 <- hasLetterAt(probes, "AACGT", c(13, 25, 25, 25, 25))
      sum(q3[ , 1] & q3[ , 2]) / sum(q3[ , 1])
      ## Probabilities to have other bases at position 25 if there is an A
      ## at position 13:
      sum(q3[ , 1] & q3[ , 3]) / sum(q3[ , 1])  # C
      sum(q3[ , 1] & q3[ , 4]) / sum(q3[ , 1])  # G
      sum(q3[ , 1] & q3[ , 5]) / sum(q3[ , 1])  # T

      ## See ?nucleotideFrequencyAt for another way to get those results.

      ## ---------------------------------------------------------------------
      ## neditAt() / isMatchingAt() / which.isMatchingAt()
      ## ---------------------------------------------------------------------
      subject <- DNAString("GTATA")

      ## Pattern "AT" matches subject "GTATA" at position 3 (exact match)
      neditAt("AT", subject, at=3)
      isMatchingAt("AT", subject, at=3)

      ## ... but not at position 1
      neditAt("AT", subject)
      isMatchingAt("AT", subject)

      ## ... unless we allow 1 mismatching letter (inexact match)
      isMatchingAt("AT", subject, max.mismatch=1)

      ## Here we look at 6 different starting positions and find 3 matches if
      ## we allow 1 mismatching letter
      isMatchingAt("AT", subject, at=0:5, max.mismatch=1)

      ## No match
      neditAt("NT", subject, at=1:4)
      isMatchingAt("NT", subject, at=1:4)

      ## 2 matches if N is interpreted as an ambiguity (fixed=FALSE)
      neditAt("NT", subject, at=1:4, fixed=FALSE)
      isMatchingAt("NT", subject, at=1:4, fixed=FALSE)

      ## max.mismatch != 0 and fixed=FALSE can be used together
      neditAt("NCA", subject, at=0:5, fixed=FALSE)
      isMatchingAt("NCA", subject, at=0:5, max.mismatch=1, fixed=FALSE)

      some_starts <- c(10:-10, NA, 6)
      subject <- DNAString("ACGTGCA")
      is_matching <- isMatchingAt("CAT", subject, at=some_starts, max.mismatch=1)
      some_starts[is_matching]

      which.isMatchingAt("CAT", subject, at=some_starts, max.mismatch=1)
      which.isMatchingAt("CAT", subject, at=some_starts, max.mismatch=1,
                         follow.index=TRUE)

      ## ---------------------------------------------------------------------
      ## WITH INDELS
      ## ---------------------------------------------------------------------
      subject <- BString("ABCDEFxxxCDEFxxxABBCDE")

      neditAt("ABCDEF", subject, at=9)
      neditAt("ABCDEF", subject, at=9, with.indels=TRUE)
      isMatchingAt("ABCDEF", subject, at=9, max.mismatch=1, with.indels=TRUE)
      isMatchingAt("ABCDEF", subject, at=9, max.mismatch=2, with.indels=TRUE)
      neditAt("ABCDEF", subject, at=17)
      neditAt("ABCDEF", subject, at=17, with.indels=TRUE)
      neditEndingAt("ABCDEF", subject, ending.at=22)
      neditEndingAt("ABCDEF", subject, ending.at=22, with.indels=TRUE)

[Package Biostrings version 2.52.0 Index]