polysat (version 0.1)

read.Tetrasat: Read Data from a TETRASAT Input File

Description

Given a file containing genotypes in the TETRASAT format, read.Tetrasat produces a vector containing the population identity of each individual as well as a two-dimensional list of vectors containing the genotypes.

Usage

read.Tetrasat(infile, missing = -9)

Arguments

infile

A character string of the file path to be read.

missing

A numerical value to be used to indicate missing data in the object produced by the function.

Value

• PopData
  An integer vector containing the population ID for each sample. Sample names are used as the names of the elements.
• Genotypes
  A two-dimensional list of integer vectors, in the standard polysat genotype format. Samples are the first dimension, and loci are the second dimension. All white space is stripped from sample names. Each vector contains all unique alleles for that sample at that locus.

Details

read.Tetrasat reads text files that are in the exact format specified by the software TETRASAT and TETRA (see references for more information). This is similar to the file format for GenePop but allows for up to four alleles per locus. All alleles must be coded by two digits. Another diference between the TETRASAT and GenePop formats is that in TETRASAT the sample name and genotypes are not separated by a comma, because the columns of data have fixed widths. Since TETRASAT files also contain information about which samples belong to which populations, a vector is also produced containing this information. The elements of the vector are numbers representing the populations, and the names of the elements are the sample names. This can be used as the popinfo argument for estimate.freq, for example, or converted to a column in an array for use in the extracols argument of write.Structure.

References

http://markwith.freehomepage.com/tetrasat.html Markwith, S. H., Stewart, D. J. and Dyer, J. L. (2006) TETRASAT: a program for the population analysis of allotetraploid microsatellite data. Molecular Ecology Notes 6, 586-589. http://ecology.bnu.edu.cn/zhangdy/TETRA/TETRA.htm Liao, W. J., Zhu, B. R., Zeng, Y. F. and Zhang, D. Y. (2008) TETRA: an improved program for population genetic analysis of allotetraploid microsatellite data. Molecular Ecology Resources 8, 1260-1262.

See Also

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

Examples

# example from the Tetrasat website
mydata <- read.Tetrasat("http://markwith.freehomepage.com/sample.txt")
mydata$PopData
mydata$Genotypes["BCRHE3",]
mydata$Genotypes[["BR6","B1_Gtype"]]

# example with defined data:
cat("Sample Data", "A1_Gtype", "A10_Gtype", "B1_Gtype", "D7_Gtype",
"D9_Gtype", "D12_Gtype", "Pop",
"BCRHE 1             0406     04040404 0208     02020202 03030303 0710",
"BCRHE 10            0406     04040404 07070707 02020202 0304     0710",
"BCRHE 2             04040404 04040404 0708     02020202 010305   0710",
"BCRHE 3             04040404 04040404 02020202 0203     03030303 0809",
"BCRHE 4             04040404 04040404 0608     0203     03030303 070910",
"BCRHE 5             04040404 04040404 0208     02020202 03030303 050710",
"BCRHE 6             0304     04040404 0207     02020202 03030303 07070707",
"BCRHE 7             0406     04040404 0708     02020202 03030303 07070707",
"BCRHE 8             0304     04040404 0203     0203     03030303 0709",
"BCRHE 9             0406     04040404 0708     02020202 03030303 0710",
"Pop",
"BR 1                0406     04040404 05050505 02020202 03030303 1012",
"BR 10               030406   04040404 0607     02020202 03030303 1011",
"BR 2                030406   04040404 07070707 02020202 03030303 09090909",
"BR 3                010304   04040404 07070707 02020202 03030303 09090909",
"BR 4                030406   04040404 07070707 0203     03030303 10101010",
"BR 5                030406   04040404 07070707 02020202 03030303 10101010",
"BR 6                0406     04040404 0507     0203     03030303 10101010",
"BR 7                0304     04040404 0809     02020202 03030303 070910",
"BR 8                030406   04040404 07070707 02020202 03030303 070910",
"BR 9                0406     04040404 07070707 02020202 03030303 07070707",
sep="", file="TetrasatExample.txt")
mydata2 <- read.Tetrasat("TetrasatExample.txt")