S4 classes for storing multiple alignments of amino acid, DNA, and RNA sequences along with algorithm metadata
Objects of these classes are returned by the multiple sequence
msaMuscle, and the
msa, all of which are
provided by the msa package.
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
print(x, show=c("alignment", "version", "call"), showNames=TRUE, showConsensus=TRUE, halfNrow=9, nameWidth=20, ...):
prints information about the object
argument allows for determining what should be printed.
show must be a character vector and may contain any
combination of the following strings:
"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).
"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
version slot is shown. If
call slot is shown.
settings of the parameters that are common to all three
multiple sequence alignment algorithms are shown. If
algorithm-specific parameters are shown.
The order in which the strings are placed in the
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
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
"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
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
or -1. Note that
msaConsensusSequence for customizing how the
consensus sequence is computed.
displays the alignment along with
metadata; synonymous to calling
displays the algorithm with which
the multiple alignment has been computed along with its
version number (see also
accessor to the
params slot (see
Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer <[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="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)
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