Saptarshi,
I know of two alternatives you can use to do fast extraction of
consecutive subsequences of a vector:
1) Fast copy: The method you mentioned of creating a memcpy'd vector
2) Pointer management: Creating an externalptr object in R and manage
the start and end of your data
If you are looking for a prototyping environment to try, I recommend
using the IRanges and Biostrings packages from the Bioconductor
project. The IRanges package contains a function called subseq for
performing 1) on all basic vector types (raw, logical, integer, etc.)
and Biostrings package contains a subseq method on an externalptr
based class that implements 2.
I was going to lobby R core members quietly about adding something
akin to subseq from IRanges into base R since it is extremely useful
for all long vectors and could replace all a:b calls with a <= b in R
code, but this publicity can't hurt.
Here is an example:
source("http://bioconductor.org/biocLite.R";)
biocLite(c("IRanges", "Biostrings"))
<< download output omitted >>
suppressMessages(library(Biostrings))
x <- rep(charToRaw("a"), 1e7)
y <- BString(rawToChar(x))
suppressMessages(library(Biostrings))
x <- rep(charToRaw("a"), 1e7)
y <- BString(rawToChar(x))
system.time(x[13:1e7])
user system elapsed
0.304 0.073 0.378
system.time(subseq(x, 13))
user system elapsed
0.011 0.007 0.019
system.time(subseq(y, 13))
user system elapsed
0.003 0.000 0.004
identical(x[13:1e7], subseq(x, 13))
[1] TRUE
identical(x[13:1e7], charToRaw(as.character(subseq(y, 13))))
[1] TRUE
sessionInfo()
R version 2.10.0 Under development (unstable) (2009-05-08 r48504)
i386-apple-darwin9.6.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.13.5 IRanges_1.3.5
loaded via a namespace (and not attached):
[1] Biobase_2.5.2
Quoting Saptarshi Guha <saptarshi.g...@gmail.com>:
Hello,
Suppose in the following code,
PROTECT(sr = R_tryEval( .... ))
sr is a RAWSXP vector. I wish to return another RAWSXP starting at
position 13 onwards (base=0).
I could create another RAWSXP of the correct length and then memcpy
the required bytes and length to this new one.
However is there a more efficient method?
Regards
Saptarshi Guha
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