GetSeq {GeneR}R Documentation

Extract regions from a sequence

Description

Return a vector of character string of regions from sequence seqno

Usage

multiExtract(seqno=0, comp = getStrand(), from=1, to=0)
getSeq(seqno=0, comp = getStrand(), from=1, to=0)
strMultiExtract(s, from=1, to=0)

Arguments

seqno Integer, sequence number. (bufseq)
s a sequence (string)
from,to Begining and ending of sequence, can be vectors. 0 represent the last nucleotide and 1 the first one.
comp Integer. If comp = 1, result will be the complement.

Value

A vector of character string, NULL if error

Author(s)

L.Cottret

Examples

s<-"cgtagtagctagctagctagctagctag"
placeString (s, seqno=1)
multiExtract(1,from=c(1,5,10),to=c(5,10,15))
#[1] "CGTAG"  "GTAGCT" "TAGCTA"

strMultiExtract(s,from=c(1,5,10),to=c(5,10,15))

# And on the reverse:
setStrand(1)
multiExtract(1,from=c(1,5,10),to=c(5,10,15))

## The reverse complement
getSeq(0,comp=1) 


[Package GeneR version 1.4.2 Index]