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 2.24.0 Index]