xscat {Biostrings} | R Documentation

## Concatenate sequences contained in XString, XStringSet and/or XStringViews objects

### Description

This function mimics the semantic of `paste(..., sep="")` but accepts XString, XStringSet or XStringViews arguments and returns an XString or XStringSet object.

### Usage

    xscat(...)

### Arguments

`...` | One or more character vectors (with no NAs), XString, XStringSet or XStringViews objects.

### Value

An XString object if all the arguments are either XString objects or character strings. An XStringSet object otherwise.

### Author(s)

H. Pagès

### See Also

XString-class, XStringSet-class, XStringViews-class, `paste`

### Examples

    ## Return a BString object:
    xscat(BString("abc"), BString("EF"))
    xscat(BString("abc"), "EF")
    xscat("abc", "EF")

    ## Return a BStringSet object:
    xscat(BStringSet("abc"), "EF")

    ## Return a DNAStringSet object:
    xscat(c("t", "a"), DNAString("N"))

    ## Arguments are recycled to the length of the longest argument:
    res1a <- xscat("x", LETTERS, c("3", "44", "555"))
    res1b <- paste0("x", LETTERS, c("3", "44", "555"))
    stopifnot(identical(as.character(res1a), as.character(res1b)))

    ## Concatenating big XStringSet objects:
    library(drosophila2probe)
    probes <- DNAStringSet(drosophila2probe)
    mm <- complement(narrow(probes, start=13, end=13))
    left <- narrow(probes, end=12)
    right <- narrow(probes, start=14)
    xscat(left, mm, right)

    ## Collapsing an XStringSet (or XStringViews) object with a small
    ## number of elements:
    probes1000 <- as.list(probes[1:1000])
    y1 <- do.call(xscat, probes1000)
    y2 <- do.call(c, probes1000)  # slightly faster than the above
    y1 == y2  # TRUE
    ## Note that this method won't be efficient when the number of
    ## elements to collapse is big (> 10000) so we need to provide a
    ## collapse() (or xscollapse()) function in Biostrings that will be
    ## efficient at doing this. Please request this on the Bioconductor
    ## mailing list (http://bioconductor.org/help/mailing-list/) if you
    ## need it.

[Package Biostrings version 2.60.2 Index]