xscat: Concatenate sequences contained in XString, XStringSet and/or...

In Bioconductor/Biostrings: Efficient manipulation of biological strings

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.

Bioconductor/Biostrings documentation built on Dec. 16, 2024, 8:46 a.m.