Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
This function mimics the semantic of paste(..., sep="")
but accepts XString, XStringSet or XStringViews
arguments and returns an XString or XStringSet object.
xscat(...)
... |
One or more character vectors (with no NAs), XString, XStringSet or XStringViews objects. |
An XString object if all the arguments are either XString objects or character strings. An XStringSet object otherwise.
H. Pagès
## 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.
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