R: Identify mutations between DNA sequences

findMutations {adegenet} | R Documentation

## Identify mutations between DNA sequences

### Description

The function `findMutations` identifies mutations (position and nature) of pairs of aligned DNA sequences. The function `graphMutations` does the same thing but plotting mutations on a directed graph.

Both functions are generics, but the only methods implemented in adegenet so far is for `DNAbin` objects.

### Usage

    findMutations(...)

    ## S3 method for class 'DNAbin'
    findMutations(x, from=NULL, to=NULL, allcomb=TRUE, ...)

    graphMutations(...)

    ## S3 method for class 'DNAbin'
    graphMutations(x, from=NULL, to=NULL, allcomb=TRUE, plot=TRUE,
                   curved.edges=TRUE, ...)

### Arguments

`x` | a `DNAbin` object containing aligned sequences, as a matrix.
`from` | a vector indicating the DNA sequences from which mutations should be found. If `NULL`, all sequences are considered (i.e., `1:nrow(x)`).
`to` | a vector indicating the DNA sequences to which mutations should be found. If `NULL`, all sequences are considered (i.e., `1:nrow(x)`).
`allcomb` | a logical indicating whether all combinations of sequences (from and to) should be considered (TRUE, default), or not (FALSE).
`plot` | a logical indicating whether the graph should be plotted.
`curved.edges` | a logical indicating whether the edges of the graph should be curved.
`...` | further arguments to be passed to other methods. Used in `graphMutations` where it is passed to the plot method for `igraph` objects.

### Value

For `findMutations`, a named list indicating the mutations from one sequence to another. For each comparison, a three-column matrix is provided, corresponding to the nucleotides in first and second sequence, and a summary of the mutation provided as: [position]:[nucleotide in first sequence]->[nucleotide in second sequence].

For `graphMutations`, a graph with the class `igraph`.

### Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk.

### See Also

The `fasta2DNAbin` to read fasta alignments with minimum RAM use.

### Examples

    ## Not run:
    data(woodmouse)

    ## mutations between first 3 sequences
    findMutations(woodmouse[1:3,])

    ## mutations from the first to sequences 2 and 3
    findMutations(woodmouse[1:3,], from=1)

    ## same, graphical display
    g <- graphMutations(woodmouse[1:3,], from=1)

    ## some manual checks
    as.character(woodmouse)[1:3,35]
    as.character(woodmouse)[1:3,36]
    as.character(woodmouse)[1:3,106]

    ## End(Not run)

[Package adegenet version 2.1.4 Index]