R: Read File in ATetra Format

read.ATetra {polysat} | R Documentation

## Read File in ATetra Format

### Description

Given a file formatted for the software ATetra, `read.ATetra` produces a `genambig` object containing genotypes, population identities, population names, and a dataset description from the file. Ploidy in the `genambig` object is automatically set to `4`.

### Usage

    read.ATetra(infile)

### Arguments

`infile` | Character string. A file path to the file to be read.

### Details

`read.ATetra` reads text files in the exact format specified by the ATetra documentation. Note that this format only allows tetraploid data and that there can be no missing data.

### Value

A `genambig` object as described above.

### Author(s)

Lindsay V. Clark

### References

http://www.vub.ac.be/APNA/ATetra_Manual-1-1.pdf

van Puyvelde, K., van Geert, A. and Triest, L. (2010) ATETRA, a new software program to analyze tetraploid microsatellite data: comparison with TETRA and TETRASAT. Molecular Ecology Resources 10, 331–334.

### See Also

`write.ATetra`, `read.Tetrasat`, `read.GeneMapper`, `read.Structure`, `read.GenoDive`, `read.SPAGeDi`, `read.POPDIST`, `read.STRand`

### Examples

    # create a file to be read
    # (this would normally be done in a text editor or with ATetra's Excel template)
    myfile <- tempfile()

    cat("TIT,Sample Rubus Data for ATetra", "LOC,1,CBA15",
    "POP,1,1,Commonwealth", "IND,1,1,1,CMW1,197,208,211,213",
    "IND,1,1,2,CMW2,197,207,211,212", "IND,1,1,3,CMW3,197,208,212,219",
    "IND,1,1,4,CMW4,197,208,212,219", "IND,1,1,5,CMW5,197,208,211,212",
    "POP,1,2,Fall Creek Lake", "IND,1,2,6,FCR4,197,207,211,212",
    "IND,1,2,7,FCR7,197,208,212,218", "IND,1,2,8,FCR14,197,207,212,218",
    "IND,1,2,9,FCR15,197,208,211,212", "IND,1,2,10,FCR16,197,208,211,212",
    "IND,1,2,11,FCR17,197,207,212,218","LOC,2,CBA23","POP,2,1,Commonwealth",
    "IND,2,1,1,CMW1,98,100,106,125","IND,2,1,2,CMW2,98,125,,",
    "IND,2,1,3,CMW3,98,126,,","IND,2,1,4,CMW4,98,106,119,127",
    "IND,2,1,5,CMW5,98,106,125,","POP,2,2,Fall Creek Lake",
    "IND,2,2,6,FCR4,98,125,,","IND,2,2,7,FCR7,98,106,126,",
    "IND,2,2,8,FCR14,98,127,,","IND,2,2,9,FCR15,98,108,117,",
    "IND,2,2,10,FCR16,98,125,,","IND,2,2,11,FCR17,98,126,,","END",
    file = myfile, sep = "\n")

    # Read the file and examine the data
    exampledata <- read.ATetra(myfile)
    summary(exampledata)
    PopNames(exampledata)
    viewGenotypes(exampledata)

[Package polysat version 1.7-6 Index]