seqinr (version 1.0-6)

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,freq=FALSE)

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)

freq

if TRUE, word frequencies are computed instead of counts

Value

• This function returns a factor whose levels are all the possible oligonucleotides. 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

citation("seqinr")

See Also

table

Examples

a=s2c("acgggtacggtcccatcgaa")
##To count dinucleotide occurrences in sequence a:
count(a,2)
##To count trinucleotide occurrences in sequence a, in frame 2:
count(a,3,2)
##To count dinucleotide frequencies in sequence a:
count(a,2,freq=TRUE)