[BioC] Using Biostring to make position frequency matrix

Valerie Obenchain vobencha at fhcrc.org
Thu Dec 5 18:17:27 CET 2013


You can use consensusMatrix().

   chr3R <- Dmelanogaster$chr3R
   pfm <- consensusMatrix(HNF4alpha)

More examples and details on the ?consensusMatrix man page.


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.
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: vobencha at fhcrc.org
Phone:  (206) 667-3158
Fax:    (206) 667-1319

More information about the Bioconductor mailing list