getSeq {GeneR}R Documentation

Sequence fragments extraction

Description

Extracts sequence fragments. getSeq further converts the fragments in character strings from the GeneR sequence buffer.

Usage


getSeq(seqno=0, strand = getStrand(), from=1, to=0)

Arguments

seqno

Integer/scalar, Sequence number (buffer number)

from, to

Integer/scalar, Absolute addresses of the begin 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)

strand

Integer/scalar, Strand (forward: 0, reverse: 1)

Value

A vector of character strings. if error : NULL

Author(s)

L.Cottret

See Also

assemble, concat, appendSeq, and for character string manipulation: substr

Examples

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


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

## The reverse complement
getSeq(1,strand=1) 


[Package GeneR version 2.24.0 Index]