Dear Johannes,
Try this:
sequences <- c("M","G","L","W","I","S","F","G","T","P","P","S","Y","T",
"Y","L","L","I","M","N","H","K","L","L","L","I","N","N","N","N","L","T","E","V",
"H","T","Y","F","N","I","N","I","N","I","D","K","M","Y","I","H","*")
indexes <- matrix(c(1,22,22,46,46,51,1,46,22,51,1,51),ncol=2,byrow=TRUE)
apply(indexes,1,function(x){
ind<- x[1]:x[2]
sequences[ind]
}
)
HTH,
Jorge
On Fri, Jan 16, 2009 at 8:06 AM, Johannes Graumann <johannes_graum...@web.de
> wrote:
> Hello,
>
> I have a list of character vectors like this:
>
> sequences <- list(
>
>
> c("M","G","L","W","I","S","F","G","T","P","P","S","Y","T","Y","L","L","I","M",
>
> "N","H","K","L","L","L","I","N","N","N","N","L","T","E","V","H","T","Y","F",
> "N","I","N","I","N","I","D","K","M","Y","I","H","*")
> )
>
> and another list of subset ranges like this:
>
> indexes <- list(
> list(
> c(1,22),c(22,46),c(46, 51),c(1,46),c(22,51),c(1,51)
> )
> )
>
> What I now want to do is to subset each entry in "sequences"
> (sequences[[1]]) with all ranges in the corresponding low level list in
> "indexes" (indexes[[1]]). Here is what I came up with.
>
> fragments <- list()
> for(iN in seq(length(sequences))){
> cat(paste(iN,"\n"))
> tmpFragments <- sapply(
> indexes[[iN]],
> function(x){
> sequences[[iN]][seq.int(x[1],x[2])]
> }
> )
> fragments[[iN]] <- tmpFragments
> }
>
> This works fine, but "sequences" contains thousands of entries and the
> corresponding "indexes" are sometimes hundreds of ranges long, so this
> whole
> process is EXTREMELY inefficient.
>
> Does somebody out there take the challenge and show me a way on how to
> speed
> this up?
>
> Thanks for any hints,
>
> Joh
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
