[BioC] kmer and zscore calculation

[Hervé Pagès]

[Oops, forgot to Cc the list when I answered this. Sending it again...]

Hi Fabrice,

The oligonucleotideFrequency() function in the Biostrings
package counts the nb of occurrences of all possible 5-mers
(use 'width=5') or 6-mers (use 'width=6'). You need to store
your sequence(s) in a DNAString or DNAStringSet object first.
On a DNAStringSet, the counts are returned in a matrix with 1
row per sequence and 1 column per k-mer:

   library(Biostrings)
   library(hgu95av2probe)
   probes <- DNAStringSet(hgu95av2probe)
   count5 <- oligonucleotideFrequency(probes, width=5)

Then:

   > dim(count5)
   [1] 201800   1024
   > count5[1:6, 1:10]
        AAAAA AAAAC AAAAG AAAAT AAACA AAACC AAACG AAACT AAAGA AAAGC
   [1,]     0     0     0     0     0     0     0     0     0     0
   [2,]     0     0     0     0     0     0     0     0     0     0
   [3,]     0     0     0     0     0     0     0     0     0     0
   [4,]     0     0     0     0     0     0     0     0     0     0
   [5,]     0     0     0     0     0     0     0     0     0     0
   [6,]     0     0     0     0     0     0     0     0     0     0

Maybe this function should have been called kmerFrequency()...

Cheers,
H.


On 12/17/2013 10:28 AM, Fabrice Tourre wrote:
> Dear list,
>
> I have a list of bed regions. each region is 10bp length. I want to
> calculate the hexamers and pentamers in theses regions and get the
> zscore. Is there any existed packages to do this?
>
> Thank you very much in advance.
>
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-- 
Hervé Pagès

Program in Computational Biology
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