[R] Fast multiple match function

[Hervé Pagès]

Hi Keshav,

findMatches() in the S4Vectors/IRanges packages (Bioconductor) I think
does what you want:

   library(IRanges)
   y <- c(16L, -3L, -2L, 15L, 15L, 0L, 8L, 15L, -2L)
   x <- c(unique(y), 999L)
   hits <- findMatches(x, y)

Then:

   > hits
   Hits object with 9 hits and 0 metadata columns:
         queryHits subjectHits
         <integer>   <integer>
     [1]         1           1
     [2]         2           2
     [3]         3           3
     [4]         3           9
     [5]         4           4
     [6]         4           5
     [7]         4           8
     [8]         5           6
     [9]         6           7
     -------
     queryLength: 7
     subjectLength: 9

The Hits object can be turned into a list with:

   > as.list(hits)
   [[1]]
   [1] 1

   [[2]]
   [1] 2

   [[3]]
   [1] 3 9

   [[4]]
   [1] 4 5 8

   [[5]]
   [1] 6

   [[6]]
   [1] 7

   [[7]]
   integer(0)

H.

 > sessionInfo()
R version 3.2.0 beta (2015-04-05 r68151)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] IRanges_2.1.43       S4Vectors_0.5.22     BiocGenerics_0.13.11

loaded via a namespace (and not attached):
[1] tools_3.2.0

On 04/06/2015 01:56 PM, Keshav Dhandhania wrote:
> Hi,
>
> I know that one can find all occurrences of x in a vector v by doing
>> which(x == v).
>
> However, if I need to do this again and again, where v is remaining the
> same, then this is quite inefficient. In my particular case, I need to do
> this millions of times, and length(v) = 100 million.
>
> Does anyone have suggestion on how to go about it?
> I know of a package called fmatch that does the above for the match
> function. But they don't handle multiple matches.
>
> Thanks
>
> 	[[alternative HTML version deleted]]
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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