[BioC] oligonucleotideTransitions from Biostrings package

Muino, Jose jose.muino at wur.nl
Sat Mar 31 17:04:59 CEST 2012

Dear all,

I have the impression that the function oligonucleotideTransitions from the Biostrings package (version 2.9) has an unexpected behavior, it only analyzes the first sequence of the DNAStringSet variable used as input.

Looking to the code of this function, I have the impression that it is just because it is using the function oligonucleotideFrequency without the parameter simplify.as set to value "collapse". Probably this parameter was added to the function oligonucleotideFrequency later than when oligonucleotideTransitions function was implemented.

This is an example of what I call an unexpected behavior (I just set the parameter left=0 to simplify the result):
> seq<-DNAStringSet(c("AAAAA","TTTTT"))
> oligonucleotideTransitions(seq,left=0)
     [,1] [,2] [,3] [,4]
[1,]    5    0    0    0

when the result should be
     [,1] [,2] [,3] [,4]
[1,]    5    0    0    5

Should forward this message to the maintainer of the Biostring package? Which is his email?

Dr. Jose M Muino
Plant Research International B.V.
Droevendaalsesteeg 1
P.O. Box 16, 6700 AA Wageningen, The Netherlands
Phone: +0317-481122.
E-mail: jose.muino at wur.nl

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