msaConsensusSequence {msa} | R Documentation

## Computation of Consensus Sequence from Multiple Alignment

### Description

This method computes a consensus sequence from a multiple alignment or a previously computed consensus matrix. Currently, two different ways of these computations are available.

### Usage

    ## S4 method for signature 'matrix'
    msaConsensusSequence(x, type=c("Biostrings", "upperlower"),
        thresh=c(80, 20), ignoreGaps=FALSE, ...)
    ## S4 method for signature 'MultipleAlignment'
    msaConsensusSequence(x, ...)

### Arguments

`x` | an object of class `MultipleAlignment` (which includes objects of classes `MsaAAMultipleAlignment`, `MsaDNAMultipleAlignment`, and `MsaRNAMultipleAlignment`) or a previously computed consensus matrix (see details below).
`type` | a character string specifying how to compute the consensus sequence. Currently, types `"Biostrings"` and `"upperlower"` are available (see details below).
`thresh` | a decreasing two-element numeric vector of numbers between 0 and 100 corresponding to the two conservation thresholds. Only relevant for `type="upperlower"` (see details below), otherwise ignored.
`ignoreGaps` | a logical (default: `FALSE`) indicating whether gaps should be considered when computing the consensus sequence. Only relevant for `type="upperlower"` (see details below), otherwise ignored.
`...` | when the method is called for a `MultipleAlignment` object, the consensus matrix is computed and, including all further arguments, passed passed on to the `msaConsensusSequence` method with signature `matrix`. The method with signature `matrix` forwards additional arguments to the `consensusString` method from the Biostrings package if `type="Biostrings"`.

### Details

The method takes a `MultipleAlignment` object or a previously computed consensus matrix and computes a consensus sequence. For `type="Biostrings"`, the method `consensusString` from the Biostrings package is used to compute the consensus sequence. For `type="upperlower"`, two thresholds (argument `thresh`, see above) are used to compute the consensus sequence:

- If the relative frequency of the most frequent letter at a given position is at least as large as the first threshold (default: 80%), then this most frequent letter is used for the consensus sequence at this position as it is.

- If the relative frequency of the most frequent letter at a given position is smaller than the first threshold, but at least as large as the second threshold (default: 20%), then this most frequent letter is used for the consensus sequence at this position, but converted to lower case.

- If the relative frequency of the most frequent letter in a column is even smaller than the second threshold, then a dot is used for the consensus sequence at this position.

- If `ignoreGaps=FALSE` (which is the default), gaps are treated like all other letters except for the fact that obviously no lowercase conversion takes place in case that the relative frequency is between the two thresholds. If `ignoreGaps=TRUE`, gaps are ignored completely, and the consensus sequence is computed from the non-gap letters only.

If the consensus matrix of a multiple alignment of nucleotide sequences contains rows labeled ‘+’ and/or ‘.’, these rows are ignored.

### Value

The function returns a character string with the consensus sequence.

### Author(s)

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`, `MsaAAMultipleAlignment`, `MsaDNAMultipleAlignment`, `MsaRNAMultipleAlignment`, `MsaMetaData`, `MultipleAlignment`, `consensusString`

### Examples

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

    ## perform multiple alignment
    myAlignment <- msa(mySeqs)

    ## regular consensus sequence using consensusString() method from the
    ## 'Biostrings' package
    msaConsensusSequence(myAlignment)

    ## use the other method
    msaConsensusSequence(myAlignment, type="upperlower")

    ## use the other method with custom parameters
    msaConsensusSequence(myAlignment, type="upperlower", thresh=c(50, 20),
                         ignoreGaps=TRUE)

    ## compute a consensus matrix first
    conMat <- consensusMatrix(myAlignment)
    msaConsensusSequence(conMat)

[Package msa version 1.22.0 Index]