exactWord {GeneR}R Documentation

Exact matches of an oligomer

Description

Gets match positions of an oligomer in fragments of a sequence

Usage

exactWord(word, seqno=0, from=1, to=0, strand = getStrand(), step=1,
  overlap=TRUE, wNbOcc =-1,case.sensitive=FALSE)

Arguments

word string/scalar, Oligomer sequence
seqno Integer/scalar, Sequence number (buffer number)
from, to Integer/scalar, Absolute addresses of the beginning and the end of the fragment, (1 means the first nucleotide and 0 conventionally the last one; from must not be larger than to and both vectors must be the same size)
step Integer/scalar, Size of the step in which search progression is done
overlap TRUE: look for overlapping oligomer
wNbOcc Integer/scalar, Maximum number of occurences to retrieve sequentially in each fragment (-1 -> all)
strand Integer/scalar, Strand (forward: 0, reverse: 1)
case.sensitive T -> difference between lower and upper case letter, F -> no difference

.

Value

A list of match positions in each fragment.
If error : NULL

Note

step with negative values will be implemented soon

Author(s)

L.Cottret

See Also

getSeq

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

placeString("TTTTTTTTTTTT")
exactWord("TTT")
exactWord("TTT",overlap=FALSE,step=2)

  

[Package GeneR version 2.6.0 Index]