polysat (version 0.1)

read.ATetra: Read File in ATetra Format

Description

Given a file formatted for the software ATetra, read.ATetra produces a vector of the population identities of each sample, as well as a two-dimensional list of vectors representing the genotypes.

Usage

read.ATetra(infile)

Arguments

infile

Character string. A file path to the file to be read.

Value

• PopData
  A numerical vector containing the population number for each sample (individual). The sample names are used as the names of this vector.
• Genotypes
  A two dimensional list of integer vectors in the standard polysat genotype format. The first dimension represents samples and the second represents loci, and both are named accordingly. Each vector contains as elements the alleles for that sample at that locus.

Details

read.ATetra reads text files in the exact format specified by the ATetra documentation. Note that this format only allows tetraploid (or lower) data and that there can be no missing data. The genotype object produced is in the same format that is produced or read by other functions in the polysat package.

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

read.Tetrasat, read.GeneMapper, read.Structure, read.GenoDive, dominant.to.codominant, write.ATetra, read.SPAGeDi

Examples

# create a file to be read
# (this would normally be done in a text editor or with ATetra's Excel template)
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 = "atetraexample.txt", sep = "")

# Read the file and examine the data
exampledata <- read.ATetra("atetraexample.txt")
exampledata$PopData
exampledata$Genotypes
exampledata$Genotypes[["CMW1","CBA23"]]