matchPWM is now part of Biostrings 2.7.47 in…

matchPWM() is now part of Biostrings 2.7.47 (in BioC devel, so you need R-2.7).

Load Biostrings:

   library(Biostrings)

Suppose 'pwm' contains a Position Weight Matrix, let's say:

   pwm <- rbind(A=c( 1,  0, 19, 20, 18,  1, 20,  7),
                C=c( 1,  0,  1,  0,  1, 18,  0,  2),
                G=c(17,  0,  0,  0,  1,  0,  0,  3),
                T=c( 1, 20,  0,  0,  0,  1,  0,  8))

Note that this is just a standard integer matrix with the 4 DNA base letters
as row names (having these row names is mandatory).
Some low-level utility functions are available for manipulating this kind of
matrix:

   > maxWeights(pwm)  # the max weight in each column
   [1] 17 20 19 20 18 18 20  8

   > maxScore(pwm)  # the max possible score
   [1] 140

Let's match 'pwm' against Human chr1:

   library(BSgenome.Hsapiens.UCSC.hg18)
   chr1 <- Hsapiens$chr1

Number of "best" matches:

   > countPWM(pwm, chr1, min.score="100%")  # takes about 5 seconds on my system
   [1] 5152

With a lower cut-off value:

   m <- matchPWM(pwm, chr1, min.score="90%")

See the 10 first matches ("first" means "smallest chromosome location", NOT "best"
matches):

   > m[1:10]
     Views on a 247249719-letter DNAString subject
   subject: TAACCCTAACCCTAACCCTAACCCTAACCCTAAC...NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
   views:
        start   end width
    [1] 31931 31938     8 [GTAAACAA]
    [2] 33324 33331     8 [GTAAACAT]
    [3] 38425 38432     8 [GTAAACAG]
    [4] 39177 39184     8 [GTAAACAC]
    [5] 46971 46978     8 [GTAAACAT]
    [6] 49952 49959     8 [GTAAACAT]
    [7] 70381 70388     8 [GTAAACAG]
    [8] 74359 74366     8 [GTAAACAC]
    [9] 90714 90721     8 [GTAAACAT]
   [10] 96544 96551     8 [GTAAACAC]

The speed could be improved, maybe by a factor 2 (or more, for longest PWMs).

Also maybe an additional argument could be added to let the user control how
the returned matches should be sorted ("left-to-right" or "best-first")?

Unlike MatInspector or the transfac-tool, there is no facility yet to suggest
individual cut-off values depending on the length of the PWMs.

See '?matchPWM' for more information (e.g. how to search the minus strand of
the chromosome).

https://stat.ethz.ch/pipermail/bioconductor/2008-April/022029.html