phyDat {phangorn}

Conversion among Sequence Formats

Description

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 'alignment'
as.phyDat(x, type = "DNA", ...)

phyDat2alignment(x)

## S3 method for class 'MultipleAlignment'
as.phyDat(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)

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.

Value

The functions return an object of class phyDat.

Author(s)

Klaus Schliep [e-mail]

See Also

[DNAbin()], [as.DNAbin()], baseFreq, glance.phyDat, read.dna, read.aa, read.nexus.data and the chapter 1 in the vignette("phangorn-specials", package="phangorn") and the example of pmlMix for the use of allSitePattern

Examples

data(Laurasiatherian)
class(Laurasiatherian)
Laurasiatherian
# transform as characters
LauraChar <- as.character(Laurasiatherian)
# and back
Laura <- phyDat(LauraChar)
all.equal(Laurasiatherian, Laura)
LauraDNAbin <- as.DNAbin(Laurasiatherian)
all.equal(Laurasiatherian, as.phyDat(LauraDNAbin))