CompoSeq {GeneR}R Documentation

Composition in mono, di or trinucleotides of a sequence

Description

Gives composition in mono, di or trinucleotides of regions (get from parameters from and to) of a sequence seqno

Usage

compoSeq(seqno=0, from=1, to=0, strand=getStrand(),
         wsize=1, p=1,allphases=TRUE)
strCompoSeq(s, wsize=1, p=1,allphases=TRUE)

Arguments

seqno Integer, sequence number. (bufseq)
s A sequence as character string
wsize Integers, size of k-uples.
from,to Begining and ending of sequence, can be vectors. 0 represent the last nucleotide and 1 the first one.
strand Strand positions
p Integer: if p=1, results are in pourcentages, else, results are in count.
allphases Flag, TRUE -> compute on all phases ; if FALSE, search will use a step = wsize.

Value

A matrix with composition for all regions.
If error: -1

Note

If setStrand changed to 1: results are with complementary.

To do: return a matrix, or a data.frame instead of a list.

See Also

exactWord

Examples

s<-"CGTACGTAGTAGCTAGCTAGCTAGCTAGCTGATCGATGCTAGCTGATCGATGCT"
placeString(s)
x<-c(1,8,15,50)
y<-c(5,12,19,54)
compoSeq(from =x, to = y,wsize=2)


[Package GeneR version 1.4.2 Index]