as.SeqFrag is called by all methods of getFrag, but not directly by the users. It creates an object sequence of class SeqFrag.
Usage
as.SeqFrag(object, begin, end, compl = FALSE, name = "frag")
is.SeqFrag(object)
Arguments
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
Value
as.SeqFrag returns a biological sequence representing by a vector of chars with the following attributes:
seqMotherthe name of the sequence from which the sequence comes
beginthe position of the first base of the fragment on the mother sequence
endthe position of the last base of the fragment on the mother sequence
classSeqFrag which is the newest class of the sequence
is.SeqFrag returns TRUE if the object is of class Seqfrag.
References
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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.