read.ATetra: Read File in ATetra Format

In lvclark/polysat: Tools for Polyploid Microsatellite Analysis

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)

lvclark/polysat documentation built on Dec. 22, 2024, 3:11 p.m.