polysat (version 0.1)

write.GeneMapper: Write Genotypes to a Table Similarly to ABI GeneMapper

Description

Given a genotype object in the standard polysat format, write.GeneMapper writes a text file of a table containing columns for sample name, locus, and alleles.

Usage

write.GeneMapper(gendata, file = "", samples = dimnames(gendata)[[1]],
loci = dimnames(gendata)[[2]])

Arguments

gendata

Genotypes in the standard polysat format: a two-dimensional list of vectors. Samples are represented in the first dimension of the list and loci in the second dimension of the list, and both dimensions are named accordingly. Each vector contains all

file

Character string. The path to which to write the file.

samples

Character vector. Samples to write to the file. This should be a subset of dimnames(gendata)[[1]].

loci

Character vector. Loci to write to the file. This should be a subset of dimnames(gendata)[[2]].

Value

• A file is written but no value is returned.

Details

Although I do not know of any population genetic software that will read this data format directly, the ABI GeneMapper Genotypes Table format is a convenient way for the user to store microsatellite genotype data and view it in a text editor or spreadsheet software. Each row contains the sample name, locus name, and alleles separated by tabs. The number of allele columns needed is automatically detected by the function by using estimate.ploidy to find the maximum number of alleles per genotype. write.GeneMapper handles missing data in a very simple way, in that it writes the missing data symbol directly to the table as though it were an allele. If you want missing data to be represented differently in the table, you can open it in spreadsheet software and use find/replace or conditional formatting to locate missing data. The file that is produced can be read back into R directly by read.GeneMapper, and therfore may be a convenient way to back up genotype data for future analysis and manipulation in polysat. (save can also be used to back up an R object more directly.) If you need to edit the genotypes and would rather do it using spreadsheet software than in polysat (e.g. mygendata[["ind1","loc3"]]<-c(122,126,134)) writing the file in GeneMapper format, editing it, then reading it back in is an option.

References

http://www.appliedbiosystems.com/genemapper

See Also

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

Examples

# create a genotype object (usually done by reading a file)
mysamples <- c("ind1", "ind2", "ind3", "ind4")
myloci <- c("loc1", "loc2")
mygendata <- array(list(-9), dim=c(4,2), dimnames=list(mysamples, myloci))
mygendata[,"loc1"] <- list(c(202,204), c(204), c(200,206,208,212),
                           c(198,204,208))
mygendata[,"loc2"] <- list(c(78,81,84), c(75,90,93,96,99), c(87), c(-9))

# write a GeneMapper file
write.GeneMapper(mygendata, "exampleGMoutput.txt")

# view the file with read.table
read.table("exampleGMoutput.txt", sep="t", header=TRUE)