MsaMetaData-class {msa} | R Documentation

## 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)

[Package msa version 1.14.0 Index]