Description Usage Arguments Author(s) See Also Examples
New multiphyDat objects can be created using new("multiphyDat", ...)
where "..." are arguments documented below.
The main input is a list of phyDat matrices. The constructor ensures that all matrices will be reordered in the same way, and genes with missing individuals will be filled by sequences of gaps ("-").
1 2 3 4 |
.Object |
the object skeleton, automatically generated when calling |
seq |
a list of phyDat matrices (1 per gene); rows should be labelled and indicate individuals, but different individuals and different orders can be used in different matrices. |
type |
a character string indicating the type of the sequences stored: "DNA" for DNA sequences, "AA" for amino-acids. |
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 |
Klaus Schliep klaus.schliep@gmail.com
Thibaut Jombart t.jombart@imperial.ac.uk
the multiphyDat class
read.multiphyDat
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | data(Laurasiatherian)
#' ## empty object
new("multiphyDat")
## simple conversion with nicely ordered output
## Not run:
genes <- list(gene1=subset(Laurasiatherian,, 1:1600, FALSE),
gene2=subset(Laurasiatherian,, 1601:3179, FALSE))
x <- new("multiphyDat", genes)
x
## End(Not run)
## trickier conversion with missing sequences / wrong order
genes <- list(gene1=subset(Laurasiatherian, 1:40),
gene2=subset(Laurasiatherian, 8:47))
x <- new("multiphyDat", genes)
x
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