seqinr (version 1.0-1)

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

� 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.

See Also

table

Examples

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)