EXP: Vectors of coefficients to compute linear forms.
Description
This dataset is used to compute linear forms on codon frequencies:
if codfreq is a vector of codon frequencies then
drop(freq %*% EXP$CG3) will return for instance the G+C content
in third codon positions. Base order is the lexical order: a,
c, g, t (or u).source
ANALSEQ EXPFILEs for command EXP.
http://biomserv.univ-lyon1.fr/doclogi/docanals/manuel.htmlDetails
It's better to work directly at the amino-acid level
when computing linear forms on amino-acid frequencies so as to have
a single coefficient vector. For instance EXP$KD to compute the Kyte
and Doolittle hydrophaty index from codon frequencies is valid only
for the standard genetic code.
An alternative for drop(freq %*% EXP$CG3) is sum( freq * EXP$CG3 ), but this is less efficient in terms of CPU
time. The advantage of the latter, however, is that thanks to
recycling rules you can use either sum( freq * EXP$A )
or sum( freq * EXP$A3 ). To do the same with the %*%
operator you have to explicit the recycling rule as in drop( freq %*% rep(EXP$A, 16)).References
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To have an overview of the seqinR's functionnality, please consult this vignette:
Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical
computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.