Hi all, I am sorry to fill your inbox mail with a naive question, although I would really appreciate your opinion. I am looking for a R function that takes a set of aligned sequences, and transforms a position frequency matrix into a position weight matrix. Thanks a lot. bogdan [[alternative HTML version deleted]]

Bogdan, Try the consensusMatrix function in the Biostrings package. It accepts a character vector, XStringSet (e.g. DNAStringSet), or an object generated by the pairwiseAlignment function: > suppressMessages(library(Biostrings)) > consensusMatrix(DNAStringSet(c("ACGT", "AAAA", "ACCT", "AGGG"))) [,1] [,2] [,3] [,4] A 4 1 1 1 C 0 2 1 0 G 0 1 2 1 T 0 0 0 2 M 0 0 0 0 R 0 0 0 0 W 0 0 0 0 S 0 0 0 0 Y 0 0 0 0 K 0 0 0 0 V 0 0 0 0 H 0 0 0 0 D 0 0 0 0 B 0 0 0 0 N 0 0 0 0 - 0 0 0 0 + 0 0 0 0 > consensusMatrix(DNAStringSet(c("ACGT", "AAAA", "ACCT", "AGGG")), baseOnly = TRUE) [,1] [,2] [,3] [,4] A 4 1 1 1 C 0 2 1 0 G 0 1 2 1 T 0 0 0 2 other 0 0 0 0 > sessionInfo() R version 2.9.0 Under development (unstable) (2009-02-23 r47990) i386-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biostrings_2.11.42 IRanges_1.1.54 loaded via a namespace (and not attached): [1] Biobase_2.3.11 Bogdan Tanasa wrote: > Hi all, > > I am sorry to fill your inbox mail with a naive question, although I would > really appreciate your opinion. > I am looking for a R function that takes a set of aligned sequences, and > transforms a position frequency > matrix into a position weight matrix. Thanks a lot. > > bogdan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >