phangorn (version 2.0.3)

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 'alignment':
as.phyDat(x, type="DNA", ...)
## S3 method for class 'MultipleAlignment':
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, ...)
## S3 method for class 'phyDat':
unique(x, incomparables = FALSE, identical = TRUE, ...)
phyDat2alignment(x)
allSitePattern(n, levels=c("a","c","g","t"), names=NULL)
acgt2ry(obj)
baseFreq(obj, freq=FALSE, all=FALSE, drop.unused.levels=FALSE)

Arguments

data

An object containing sequences.

x

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). Several popular formats are supported: "phylip", "interleaved", "sequential", "clustal", "fasta" or "nexus", or any unambiguous abbreviation of these.

n

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

all

all a logical; if all = TRUE, all counts of bases, ambiguous codes, missing data, and alignment gaps are returned as defined in the contrast.

drop.unused.levels

logical, drop unused levels

incomparables

for compatability with unique.

identical

if TRUE (default) sequences have to be identical, if FALSE sequences are considered duplicates if distance between sequences is zero (happens frequently with ambiguous sites).

...

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. There is a more detailed example for specifying "USER" defined data formats in the vignette "phangorn-specials".

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.

See Also

DNAbin, as.DNAbin, 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
baseFreq(Laurasiatherian)
baseFreq(Laurasiatherian, all=TRUE)
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)