ExactWord {GeneR} | R Documentation |
Get positions in regions of the sequence where motif was found
exactWord(word, seqno=0, from=1, to=0, step=1,wNbOcc =-1, comp = getStrand())
seqno |
Integer, sequence number (bufseq) |
word |
Motif to look for |
from,to |
Begining and ending of regions to study, can be vectors. 0 represent the last nucleotide and 1 the first one. |
step |
Scalar. Size of step in which progression is done. Can be negative. |
wNbOcc |
boolean. T -> return all occurences in each regions. F -> Return first occurence. |
comp |
Integer. If comp = 1, result will be the complement. |
A list with all positions for each regions. |
|
If nothing found: -1 |
|
If regions limits unvalid: NA |
L.Cottret
s<-"cgtagctagctagctagctagctagctagcta" placeString(s) exactWord(word="ag", from=c(3,11,23),to=c(9,17,29)) #[[1]] #[1] 4 8 # #[[2]] #[1] 12 16 # #[[3]] #[1] 24 28