as.phyDat: Conversion among Sequence Formats

In phangorn: Phylogenetic Reconstruction and Analysis

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 '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)

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.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))

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.