findMutations | R Documentation |
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.
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, ...)
x |
a |
from |
a vector indicating the DNA sequences from which mutations
should be found. If |
to |
a vector indicating the DNA sequences to which mutations
should be found. If |
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
|
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
.
Thibaut Jombart t.jombart@imperial.ac.uk.
The fasta2DNAbin
to read fasta alignments with minimum
RAM use.
## 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)
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