XStringSet-comparison {Biostrings} | R Documentation

## Comparing and ordering the elements in one or more XStringSet objects

### Description

Methods for comparing and ordering the elements in one or more XStringSet objects.

### Details

Element-wise (aka "parallel") comparison of 2 XStringSet objects is based on the lexicographic order between 2 BString, DNAString, RNAString, or AAString objects.

For DNAStringSet and RNAStringSet objects, the letters in the respective alphabets (i.e. DNA_ALPHABET and RNA_ALPHABET) are ordered based on a predefined code assigned to each letter. The code assigned to each letter can be retrieved with:

      dna_codes <- as.integer(DNAString(paste(DNA_ALPHABET, collapse="")))
      names(dna_codes) <- DNA_ALPHABET

      rna_codes <- as.integer(RNAString(paste(RNA_ALPHABET, collapse="")))
      names(rna_codes) <- RNA_ALPHABET

Note that this order does NOT depend on the locale in use. Also note that comparing DNA sequences with RNA sequences is supported and in that case T and U are considered to be the same letter.

For BStringSet and AAStringSet objects, the alphabetical order is defined by the C collation. Note that, at the moment, AAStringSet objects are treated like BStringSet objects i.e. the alphabetical order is NOT defined by the order of the letters in AA_ALPHABET. This might change at some point.

### `pcompare()` and related methods

In the code snippets below, `x` and `y` are XStringSet objects.

  `pcompare(x, y)`: Performs element-wise (aka "parallel") comparison of `x` and `y`, that is, returns an integer vector where the i-th element is less than, equal to, or greater than zero if the i-th element in `x` is considered to be respectively less than, equal to, or greater than the i-th element in `y`. If `x` and `y` don't have the same length, then the shortest is recycled to the length of the longest (the standard recycling rules apply).

  `x == y`, `x != y`, `x <= y`, `x >= y`, `x < y`, `x > y`: Equivalent to `pcompare(x, y) == 0`, `pcompare(x, y) != 0`, `pcompare(x, y) <= 0`, `pcompare(x, y) >= 0`, `pcompare(x, y) < 0`, and `pcompare(x, y) > 0`, respectively.

### `order()` and related methods

In the code snippets below, `x` is an XStringSet object.

  `is.unsorted(x, strictly=FALSE)`: Return a logical values specifying if `x` is unsorted. The `strictly` argument takes logical value indicating if the check should be for _strictly_ increasing values.

  `order(x, decreasing=FALSE)`: Return a permutation which rearranges `x` into ascending or descending order.

  `rank(x, ties.method=c("first", "min"))`: Rank `x` in ascending order.

  `sort(x, decreasing=FALSE)`: Sort `x` into ascending or descending order.

### `duplicated()` and `unique()`

In the code snippets below, `x` is an XStringSet object.

  `duplicated(x)`: Return a logical vector whose elements denotes duplicates in `x`.

  `unique(x)`: Return the subset of `x` made of its unique elements.

### `match()` and `%in%`

In the code snippets below, `x` and `table` are XStringSet objects.

  `match(x, table, nomatch=NA_integer_)`: Returns an integer vector containing the first positions of an identical match in `table` for the elements in `x`.

  `x %in% table`: Returns a logical vector indicating which elements in `x` match identically with an element in `table`.

### `is.na()` and related methods

In the code snippets below, `x` is an XStringSet object. An `XStringSet` object never contains missing values (these methods exist for compatibility).

  `is.na(x)`: Returns `FALSE` for every element.

  `anyNA(x)`: Returns `FALSE`.

### Author(s)

H. Pagès

### See Also

XStringSet-class, `==`, `is.unsorted`, `order`, `rank`, `sort`, `duplicated`, `unique`, `match`, `%in%`

### Examples

    ## ---------------------------------------------------------------------
    ## A. SIMPLE EXAMPLES
    ## ---------------------------------------------------------------------

    dna <- DNAStringSet(c("AAA", "TC", "", "TC", "AAA", "CAAC", "G"))
    match(c("", "G", "AA", "TC"), dna)

    library(drosophila2probe)
    fly_probes <- DNAStringSet(drosophila2probe)
    sum(duplicated(fly_probes))  # 481 duplicated probes

    is.unsorted(fly_probes)  # TRUE
    fly_probes <- sort(fly_probes)
    is.unsorted(fly_probes)  # FALSE
    is.unsorted(fly_probes, strictly=TRUE)  # TRUE, because of duplicates
    is.unsorted(unique(fly_probes), strictly=TRUE)  # FALSE

    ## Nb of probes that are the reverse complement of another probe:
    nb1 <- sum(reverseComplement(fly_probes) %in% fly_probes)
    stopifnot(identical(nb1, 455L))  # 455 probes

    ## Probes shared between drosophila2probe and hgu95av2probe:
    library(hgu95av2probe)
    human_probes <- DNAStringSet(hgu95av2probe)
    m <- match(fly_probes, human_probes)
    stopifnot(identical(sum(!is.na(m)), 493L))  # 493 shared probes

    ## ---------------------------------------------------------------------
    ## B. AN ADVANCED EXAMPLE
    ## ---------------------------------------------------------------------
    ## We want to compare the first 5 bases with the 5 last bases of each
    ## probe in drosophila2probe. More precisely, we want to compute the
    ## percentage of probes for which the first 5 bases are the reverse
    ## complement of the 5 last bases.

    library(drosophila2probe)
    probes <- DNAStringSet(drosophila2probe)

    first5 <- narrow(probes, end=5)
    last5 <- narrow(probes, start=-5)
    nb2 <- sum(first5 == reverseComplement(last5))
    stopifnot(identical(nb2, 17L))

    ## Percentage:
    100 * nb2 / length(probes)  # 0.0064 %

    ## If the probes were random DNA sequences, a probe would have 1 chance
    ## out of 4^5 to have this property so the percentage would be:
    100 / 4^5  # 0.098 %

    ## With randomly generated probes:
    set.seed(33)
    random_dna <- sample(DNAString(paste(DNA_BASES, collapse="")),
                         sum(width(probes)), replace=TRUE)
    random_probes <- successiveViews(random_dna, width(probes))
    random_probes
    random_probes <- as(random_probes, "XStringSet")
    random_probes

    random_first5 <- narrow(random_probes, end=5)
    random_last5 <- narrow(random_probes, start=-5)

    nb3 <- sum(random_first5 == reverseComplement(random_last5))
    100 * nb3 / length(random_probes)  # 0.099 %

[Package Biostrings version 2.60.2 Index]