Concat {GeneR}R Documentation

Concatenation of two sequences

Description

Concatenates a fragment of one sequence with a fragment of another one.

Usage

concat(seqno1=0, seqno2=1, destSeqno=2, from1=1, to1=0, strand1=getStrand(),
from2=1, to2=0, strand2=getStrand())

Arguments

seqno1

Integer/scalar, Integer/scalar, First sequence number (buffer number)

seqno2

Integer/scalar, Integer/scalar, Second sequence number (buffer number)

destSeqno

Integer/scalar, Output sequence number (buffer number)

strand1

Integer/scalar, Strand of the first fragment (forward: 0, reverse: 1)

from1,to1

Integer/scalar, Absolute addresses of the beginning and the end of the first 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).

from2,to2

Integer/scalar, Absolute addresses of the beginning and the end of the second 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)

strand2

Integer/scalar, Strand of the second fragment (forward: 0, reverse: 1)

Value

destSeq or -1 if error

Author(s)

L.Cottret

See Also

assemble, getSeq, appendSeq

Examples


s1<- "aaacgctagcgcg"
placeString(s1)
s2<-"ttttctatcag"
placeString(s2,1)
concat(seqno1=0,seqno2=1, from1=2,to1=3,from2=8,to2=0, strand1=1)
getSeq(2)
#[1] "TTTCAG"
  

[Package GeneR version 2.24.0 Index]