ExactWord {GeneR}R Documentation

Look for motifs in a sequence

Description

Get positions in regions of the sequence where motif was found

Usage

exactWord(word, seqno=0, from=1, to=0, step=1,wNbOcc =-1, comp = getStrand())

Arguments

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.

Value

A list with all positions for each regions.
If nothing found: -1
If regions limits unvalid: NA

Author(s)

L.Cottret

See Also

multiExtract

Examples

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
  

[Package GeneR version 1.4.2 Index]