count: Composition of dimer/trimer/etc nucleotides
Description
Counts the number of times dimer/trimer/etc nucleotides occurs in a
sequence. Note that the oligomers are overlapping.
Usage
count(seq,word,frame=0)
Arguments
seq
a vector of chars
word
an integer giving the size of word (n-mer) to count
frame
an integer (0,1,2) giving the frame (starting position)
Value
This function returns a factor whose levels are all the possible
oligonucleotids. All oligomers are returned, even if absent from the sequence.
Details
count counts the occurence of all words by moving a window of
length word. The window step is always an unit. frame
controls the starting position in the sequence for the count.
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.
a=s2c("acgggtacggtcccatcgaa")
##To count the occurences of dinucleotides of a:count(a,2)
##To count the occurences of trinucleotides of a in frame 2:count(a,3,2)