adegenet: mutations – R documentation

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mutations

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.

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)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release