[BioC] Using Biostring to make position frequency matrix

[Valerie Obenchain]

Hi,

You can use consensusMatrix().

   library(Biostrings)
   data(HNF4alpha)
   library(BSgenome.Dmelanogaster.UCSC.dm3)
   chr3R <- Dmelanogaster$chr3R
   pfm <- consensusMatrix(HNF4alpha)

More examples and details on the ?consensusMatrix man page.

Valerie

On 12/04/2013 04:13 PM, Fabrice Tourre wrote:
> Dear list,
>
> There is a PWM function in Biostring to make  position weight matrix.
> How can I make a  position frequency matrix with Biostring? Thank you.
>
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