SeqFastaAA {seqinr} | R Documentation |
as.SeqFastaAA
is called by the function as read.fasta
. It creates an object of class SeqFastaAA
.
is.SeqFastaAA
returns TRUE if the object is of class SeqFastaAA
.
summary.SeqFastaAA
gives the AA composition of an object of class SeqFastaAA
.
as.SeqFastaAA(object, name = NULL, Annot = NULL) is.SeqFastaAA(object) summary.SeqFastaAA(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.SeqFastaAA
returns an object sequence of class SeqFastaAA
.
summary.SeqFastaAA
returns a list which the following components:
composition |
the AA counting of the sequence |
AA.Property |
the percentage of each group of amino acid in the sequence. By example, the groups are small, tiny, aliphatic, aromatic ... |
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/seqAA.fasta",package="seqinr"),seqtype="AA") is.SeqFastaAA(s[[1]]) summary(s[[1]]) myseq = s2c("MSPTAYRRGSPAFLV*") as.SeqFastaAA(myseq, name = "myseq", Annot = "blablabla") myseq