SeqFrag {seqinr} | R Documentation |
as.SeqFrag
is called by all methods of getFrag
, but not directly by the users. It creates an object sequence of class SeqFrag
.
as.SeqFrag(object, begin, end, compl = FALSE, name = "frag") is.SeqFrag(object)
object |
an object sequence of class seqFastadna , seqFastaAA , seqAcnucWeb or seqFrag |
begin |
the first base of the fragment to get |
end |
the last base of the fragment to get |
compl |
if TRUE, you must give a name for the sequence |
name |
the name of the fragment of the sequence |
as.SeqFrag
returns a biological sequence representing by a vector of chars with the following attributes:
seqMother |
the name of the sequence from which the sequence comes |
begin |
the position of the first base of the fragment on the mother sequence |
end |
the position of the last base of the fragment on the mother sequence |
class |
SeqFrag which is the newest class of the sequence |
is.SeqFrag
returns TRUE if the object is of class Seqfrag.
D. Charif
To have an overview of the seqinR's functionnality, please consult this vignette:
Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical
computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.
s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr")) getFrag(s[[1]],1,10)