phyDat: 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, ...) 
read.phyDat(file, format="phylip", type="DNA", ...)
write.phyDat(x, file, format="phylip",...)
## S3 method for class 'DNAbin':
as.phyDat(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':
subset(x, subset, select, site.pattern = TRUE, ...)
allSitePattern(n, levels=c("a","c","g","t"), names=NULL)
acgt2ry(obj)
baseFreq(obj, freq=FALSE, drop.unused.levels=FALSE)

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.

file

A file name.

format

File format of the sequence alignment (see details).

Number of sequences.

names

Names of sequences.

subset

a subset of taxa.

select

a subset of characters.

site.pattern

select site pattern or sites.

allLevels

return original data.

obj

as object of class phyDat

freq

logical, if 'TRUE', frequencies or counts are returned otherwise proportions

drop.unused.levels

logical, drop unused levels

...

further arguments passed to or from other methods.

Value

The functions return an 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. allSitePattern returns all possible site patterns and can be useful in simulation studies. For further details see the vignette phangorn-specials. write.phyDat calls the function write.dna or write.nexus.data and read.phyDat calls the function read.dna, read.aa or read.nexus.data see for more details over there. You may import data directly with read.dna or read.nexus.data and convert the data to class phyDat. The generic function c can be used to to combine sequences and unique to get all unique sequences or unique haplotypes. acgt2ry converts a phyDat object of nucleotides into an binary ry-coded dataset. There is a more detailed example for specifying USER defined data formats in the vignette advanced features.

Examples

Run this code

data(Laurasiatherian)
class(Laurasiatherian)
Laurasiatherian
baseFreq(Laurasiatherian)
subset(Laurasiatherian, subset=1:5)
# transform into old ape format
LauraChar <- as.character(Laurasiatherian)
# and back 
Laura <- phyDat(LauraChar, return.index=TRUE)
all.equal(Laurasiatherian, Laura)
allSitePattern(5)

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