Class MsaMetaData

Description

S4 class for storing metadata about multiple sequence alignment results

Objects

Objects of this virtual class are not be created and used directly. This is an auxiliary class used by the classes MsaAAMultipleAlignment, MsaDNAMultipleAlignment, and MsaRNAMultipleAlignment

Slots

The following slots are defined for MsaMetaData objects:

version:

slot in which information is stored with which algorithm the multiple alignment has been computed along with its version number.

params:

list in which the parameters are stored with which the multiple alignment algorithm has been executed.

call:

the matched call with which the object was created

Methods

version(object):

accessor to the version slot

params(x):

accessor to the params slot

Author(s)

Enrico Bonatesta and Christoph Horejs-Kainrath <msa@bioinf.jku.at>

References

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.

See Also

msa, msaClustalW, msaClustalOmega, msaMuscle, MsaAAMultipleAlignment, MsaDNAMultipleAlignment, MsaRNAMultipleAlignment

Examples

## read sequences
filepath <- system.file("examples", "exampleAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)

## simple call with default values
myAlignment <- msaClustalOmega(mySeqs)

## show the algorithm version with which the results were created
version(myAlignment)

## show the results
show(myAlignment)

## print the results
print(myAlignment, show="alignment")
print(myAlignment, show=c("alignment", "version"))
print(myAlignment, show="standardParams")
print(myAlignment, show="algParams")
print(myAlignment, show=c("call", "version"))

## show the params
params(myAlignment)