Classes MsaAAMultipleAlignment, MsaDNAMultipleAlignment, and MsaRNAMultipleAlignment

Description

S4 classes for storing multiple alignments of amino acid, DNA, and RNA sequences along with algorithm metadata

Objects

Objects of these classes are returned by the multiple sequence alignment algorithms msaClustalW, msaClustalOmega, msaMuscle, and the wrapper function msa, all of which are provided by the msa package.

Details

The class MsaAAMultipleAlignment extends the AAMultipleAlignment class, the class MsaDNAMultipleAlignment extends the DNAMultipleAlignment class, and the class MsaRNAMultipleAlignment extends the RNAMultipleAlignment class. All three classes extend their parent classes by the slots contained in the MsaMetaData, i.e. all three classes are class unions of the aforementioned parent classes and the class MsaMetaData.

Methods

print(x, show=c("alignment", "version", "call"), showNames=TRUE, showConsensus=TRUE, halfNrow=9, nameWidth=20, ...):

prints information about the object x; the show argument allows for determining what should be printed. The show must be a character vector and may contain any combination of the following strings: if show contains "alignment", the multiple sequence alignment is printed in a way similar to the corresponding method from the Biostrings package (except for the consensus sequence, see below). If show contains "complete", the entire width of the alignment is printed by splitting it over multiple blocks of lines if necessary. This overrules "alignment" if both are contained in the show argument. If show contains "version", the version slot is shown. If show contains "call", the call slot is shown. If show contains "standardParams", the settings of the parameters that are common to all three multiple sequence alignment algorithms are shown. If show contains "algParams", the algorithm-specific parameters are shown. The order in which the strings are placed in the show argument does not have an effect on the order in which data are printed. The default is show=c("alignment", "version", "call"), i.e. by default, the multiple sequence alignment is shown along with version and call information. If show contains "all", the complete alignment is shown along with version information, call, and the complete set of parameters. As said above, by default, printing alignments is similar to the standard print method provided by the Biostrings package, whereas including "complete" in the argument show prints the entire width of the alignment. Unlike the method from the Biostrings package, the appearance can be customized: by default, the consensus sequence is appended below the alignment. To switch this off, use showConsensus=FALSE. Whether or not sequence names should be printed can be controlled via the showNames argument. The width reserved for the sequence names can be adjusted using the nameWidth argument; the default is 20 like in the Biostrings method. If the number of sequences in the alignment is large, output can become quite lengthy. That is why only the first halfNrow and the last halfNrow sequences are shown. To show all sequences, set halfNrow to NA or -1. Note that print can also handle masked objects, where the masked sequences/positions are shown as hash marks. However, the consensus sequences are computed from the complete, unmasked alignment and displayed as such. Additional arguments are passed on to msaConsensusSequence for customizing how the consensus sequence is computed.

show(object):

displays the alignment along with metadata; synonymous to calling print with default arguments.

version(object):

displays the algorithm with which the multiple alignment has been computed along with its version number (see also MsaMetaData).

params(x):

accessor to the params slot (see also MsaMetaData)

Author(s)

Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer <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, MsaMetaData

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="alignment", showConsensus=FALSE)
print(myAlignment, show=c("alignment", "version"))
print(myAlignment, show="standardParams")
print(myAlignment, show="algParams")
print(myAlignment, show=c("call", "version"))

## print results with custom consensus sequence
print(myAlignment, show="complete", type="upperlower", thresh=c(50, 20))

## show the params
params(myAlignment)