Description Usage Arguments Author(s) See Also Examples
New multidna objects can be created using new("multidna", ...)
where "..." are arguments documented below.
The main input is a list of DNAbin matrices. The constructor ensures that all matrices will be reordered in the same way, and as an option (setting add.gaps=TRUE
, gap-only sequences ("...—–...") will be added wherever sequences are missing.
1 2 3 |
.Object |
the object skeleton, automatically generated when calling |
dna |
a list of DNAbin matrices (1 per gene); rows should be labelled and indicate individuals, but different individuals and different orders can be used in different matrices. |
ind.info |
an optional data.frame containing information on the individuals, where individuals are in rows. |
gene.info |
an optional data.frame containing information on the genes, where genes are in rows. |
add.gaps |
a logical indicating if gap-only sequences should be used where sequences are missing; defaults to TRUE. |
quiet |
a logical indicating if messages should be shown; defaults to FALSE. |
... |
further arguments to be passed to other methods |
Thibaut Jombart t.jombart@imperial.ac.uk
the multidna class
read.multidna
and read.multidna
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## empty object
new("multidna")
## simple conversion with nicely ordered output
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
x
image(woodmouse)
image(x@dna[[1]])
image(x@dna[[2]])
## trickier conversion with missing sequences / wrong order
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[c(5:1,14:15),501:965])
x <- new("multidna", genes)
x
image(x@dna[[1]])
image(x@dna[[2]])
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