S4 class for storing metadata about multiple sequence alignment results
Objects of this virtual class are not be created and used directly. This
is an auxiliary class used by the classes
The following slots are defined for
slot in which information is stored with which algorithm the multiple alignment has been computed along with its version number.
list in which the parameters are stored with which the multiple alignment algorithm has been executed.
the matched call with which the object was created
accessor to the
accessor to the
Enrico Bonatesta and Christoph Horejs-Kainrath <[email protected]>
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.
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## 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)
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