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Muino, Jose
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@muino-jose-5198
Last seen 9.6 years ago
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?
Thanks,
Jose
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
http://www.pri.wur.nl