CompoSeq {GeneR} | R Documentation |
Gives composition in mono, di or trinucleotides of regions (get from parameters from and to) of a sequence seqno
compoSeq(seqno=0, from=1, to=0, strand=getStrand(), wsize=1, p=1,allphases=TRUE) strCompoSeq(s, wsize=1, p=1,allphases=TRUE)
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. |
A matrix with composition for all regions.
If error: -1
If setStrand changed to 1: results are with complementary.
To do: return a matrix, or a data.frame instead of a list.
s<-"CGTACGTAGTAGCTAGCTAGCTAGCTAGCTGATCGATGCTAGCTGATCGATGCT" placeString(s) x<-c(1,8,15,50) y<-c(5,12,19,54) compoSeq(from =x, to = y,wsize=2)