lowlevel-matching: Low-level matching functions
In Biostrings: Efficient manipulation of biological strings

Description Usage Arguments Details Value See Also Examples

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.

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)

`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".

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.

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:

1
2
3

    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:

1 2	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:

1
2
3

    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:

1 2	which(isMatchingAt(...))[1]

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

1
2
3

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

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

1 2	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.

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

  ## ---------------------------------------------------------------------
  ## 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)