msaConvert {msa} | R Documentation |
This function converts a multiple sequence alignment object to formats used in other sequence analysis packages.
msaConvert(x, type=c("seqinr::alignment", "bios2mds::align", "ape::AAbin", "ape::DNAbin", "phangorn::phyDat", "bio3d::fasta"))
x |
an object of class |
type |
a character string specifying to which type of object
|
The function converts x
to the class of object as
specified by the type
argument. The values possible
for the type
argument follow the same principle
pkg::cl, i.e. x
is converted to class
cl as defined in the pkg package.
The conversions for usage by the packages seqinr,
bios2mds, and ape work independently of these
packages and do not strictly require these packages. They
need not even be installed. This approach has been chosen
to avoid abundant dependencies and possible incompatibilities.
That is also why the standard S3/S4 mechanism of
as
/as.class
functions is not used.
The conversion to the phyDat
class can be done
easily using the as.phyDat
function from the
phangorn package. The msaConvert
function
still provides this conversion for the sake of consistency.
However, this conversion is just a wrapper function around
the as.phyDat
function from the phangorn
package. Thus, the phangorn package needs to be installed.
The conversion "ape::AAbin"
only works for multiple alignments of amino acid sequences,
while the conversions "ape::DNAbin"
and
"phangorn::phyDat"
only work for multiple alignments
of DNA sequences. When converting to "ape::AAbin"
,
gaps/dashes are replaced by ‘X’. Moreover, conversions
to "ape::DNAbin"
also convert all characters to
lowercase and replace gaps/dashes by ‘n’.
The function returns an object of the class as specified by
the type
argument.
Ulrich Bodenhofer <msa@bioinf.jku.at>
http://www.bioinf.jku.at/software/msa
U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.
msa
, MsaAAMultipleAlignment
,
MsaDNAMultipleAlignment
,
MsaRNAMultipleAlignment
,
MsaMetaData
## read sequences filepath <- system.file("examples", "exampleAA.fasta", package="msa") mySeqs <- readAAStringSet(filepath) ## perform multiple alignment myAlignment <- msa(mySeqs) ## convert to an object of class 'alignment' (package 'seqinr') msaConvert(myAlignment, "seqinr::alignment") ## convert to an object of class 'align' (package 'bios2mds') msaConvert(myAlignment, "bios2mds::align")