R: Conversion among Sequence Formats

phyDat {phangorn} | R Documentation

## 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, ...)

    dna2codon(x)

    codon2dna(x)

    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.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, ...)

    write.phyDat(x, file, format = "phylip", colsep = "", nbcol = -1, ...)

    read.phyDat(file, format = "phylip", type = "DNA", ...)

    baseFreq(obj, freq = FALSE, all = FALSE, drop.unused.levels = FALSE)

    ## S3 method for class 'phyDat'
    subset(x, subset, select, site.pattern = TRUE, ...)

    ## S3 method for class 'phyDat'
    unique(x, incomparables = FALSE, identical = TRUE, ...)

    allSitePattern(n, levels = c("a", "c", "g", "t"), names = NULL)

    genlight2phyDat(x, ambiguity = NA)

    ## S3 method for class 'phyDat'
    image(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.
`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.
`colsep` | a character used to separate the columns (a single space by default).
`nbcol` | a numeric specifying the number of columns per row (-1 by default); may be negative implying that the nucleotides are printed on a single line.
`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
`subset` | a subset of taxa.
`select` | a subset of characters.
`site.pattern` | select site pattern or sites.
`incomparables` | for compatibility 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).
`n` | Number of sequences.
`names` | Names of sequences.
`ambiguity` | character for ambiguous character and no contrast is provided.

### 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.

### Value

The functions return an object of class `phyDat`.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### 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)
    all.equal(Laurasiatherian, Laura)
    allSitePattern(5)

[Package phangorn version 2.3.1 Index]