These functions transform several DNA formats into the phyDat format.
allSitePattern generates an alignment of all possible site patterns.
Usage
phyDat(data, type = "DNA", levels = NULL, return.index = TRUE, ...)
as.phyDat(x, ...)
# S3 method for class 'factor'
as.phyDat(x, ...)
# S3 method for class 'DNAbin'
as.phyDat(x, ...)
# S3 method for class 'AAbin'
as.phyDat(x, ...)
# S3 method for class 'alignment'
as.phyDat(x, type = "DNA", ...)
phyDat2alignment(x)
# S3 method for class 'MultipleAlignment'
as.phyDat(x, ...)
# S3 method for class 'AAStringSet'
as.phyDat(x, ...)
# S3 method for class 'DNAStringSet'
as.phyDat(x, ...)
as.StringSet(x, ...)
# S3 method for class 'phyDat'
as.StringSet(x, ...)
# S3 method for class 'phyDat'
as.MultipleAlignment(x, ...)
# S3 method for class 'phyDat'
as.character(x, allLevels = TRUE, ...)
# S3 method for class 'phyDat'
as.data.frame(x, ...)
# S3 method for class 'phyDat'
as.DNAbin(x, ...)
# S3 method for class 'phyDat'
as.AAbin(x, ...)
genlight2phyDat(x, ambiguity = NA)
acgt2ry(obj)
unalign(x)Arguments
- data
An object containing sequences.
- type
Type of sequences ("DNA", "AA", "CODON" or "USER").
- levels
Level attributes.
- return.index
If TRUE returns a index of the site patterns.
- ...
further arguments passed to or from other methods.
- x
An object containing sequences.
- allLevels
return original data.
- ambiguity
character for ambiguous character and no contrast is provided.
- obj
as object of class phyDat
Details
If type "USER" a vector has to be give to levels. For example
c("a", "c", "g", "t", "-") would create a data object that can be used in
phylogenetic analysis with gaps as fifth state. There is a more detailed
example for specifying "USER" defined data formats in the vignette
"phangorn-specials".
acgt2ry converts a phyDat object of nucleotides into an binary
ry-coded dataset.
unalign converts a phyDat object of nucleotides or amino acids
into a DNAbin or AAbin object in list form removing all gaps.
These objects can be exported using write.FASTA.
See also
DNAbin, as.DNAbin,
baseFreq, glance.phyDat,
read.dna, read.nexus.data
and the chapter 1 in the vignette("phangorn-specials",
package="phangorn") and the example of pmlMix for the use of
allSitePattern
Author
Klaus Schliep klaus.schliep@gmail.com
Examples
data(Laurasiatherian)
class(Laurasiatherian)
#> [1] "phyDat"
Laurasiatherian
#> 47 sequences with 3179 character and 1605 different site patterns.
#> The states are a c g t
# transform as characters
LauraChar <- as.character(Laurasiatherian)
# and back
Laura <- phyDat(LauraChar)
all.equal(Laurasiatherian, Laura)
#> [1] TRUE
LauraDNAbin <- as.DNAbin(Laurasiatherian)
all.equal(Laurasiatherian, as.phyDat(LauraDNAbin))
#> [1] TRUE