SeqFastadna {seqinr} | R Documentation |
as.SeqFastadna
is called by many functions as read.fasta
. It creates an object of class SeqFastadna
.
is.SeqFastadna
returns TRUE if the object is of class SeqFastadna
.
summary.SeqFastadna
gives the base composition of an object of class SeqFastadna
.
as.SeqFastadna(object, name = NULL, Annot = NULL) is.SeqFastadna(object) summary.SeqFastadna(object,...)
object |
a vector of chars representing a biological sequence |
name |
NULL a character string specifying a name for the sequence |
Annot |
NULL a character string specifying some annotations for the sequence |
... |
additional arguments affecting the summary produced |
as.SeqFastadna
returns an object sequence of class SeqFastadna
.
summary.SeqFastadna
returns a list which the following components:
length |
the legth of the sequence |
compo |
the base counting of the sequence |
GC |
the percentage of G+C in the sequence |
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(system.file("sequences/malM.fasta",package="seqinr")) is.SeqFastadna(s[[1]]) summary(s[[1]]) myseq = s2c("acgttgatgctagctagcatcgat") as.SeqFastadna(myseq, name = "myseq", Annot = "blablabla") myseq