getSeq {GeneR} | R Documentation |
Extracts sequence fragments. getSeq further converts the fragments in character strings from the GeneR sequence buffer.
getSeq(seqno=0, strand = getStrand(), from=1, to=0)
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) |
A vector of character strings. if error : NULL
L.Cottret
assemble
, concat
,
appendSeq
, and for character string manipulation: substr
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)