polysat (version 0.1)

read.SPAGeDi: Read Genotypes in SPAGeDi format

Description

read.SPAGeDi can read a text file formatted for the SPAGeDi software and return a genotype object in the standard polysat format, as well as optionally returning a vector of individual ploidies and/or a data frame of categories and spatial coordinates.

Usage

read.SPAGeDi(infile, allelesep = "/", returncatspatcoord = FALSE,
             returnploidies = FALSE, missing = -9)

Arguments

infile

Character string. Path of the file to read.

allelesep

The character that is used to delimit alleles within genotypes, or "" if alleles have a fixed number of digits and are not delimited by any character. Other examples shown in section 3.2.1 of the SPAGeDi 1.3 manual include "/"

returncatspatcoord

Boolean. Indicates whether a data frame should be returned containing the category and spatial coordinates columns.

returnploidies

Boolean. Indicates whether a vector should be returned containing the ploidy of each individual.

missing

The symbol to be used to specify missing data in the genotype object that is returned.

Value

• Under the default where returncatspatcoord=FALSE and returnploidies=FALSE, a genotype object in the standard polysat format is returned. This is a two-dimensional list of integer vectors, where the first dimension of the list represents samples and the second dimension of the list represents loci. Both dimensions are named by the individual and locus names found in the file. Each vector contains all unique alleles, formatted as integers. Otherwise, a list of two or three objects is returned:
• CatSpatCoord
  A data frame of categories and spatial coordinates, unchanged from the file. The format of each column is determined under the default read.table settings. Row names are individual names from the file. Column names are the same as in the file.
• Indploidies
  A vector containing the ploidy of each individual, as determined by the (maximum) number of alleles per genotype, including zeros on the right. The vector is named by the individual names from the file.
• Genotypes
  A genotype object as described above.

Details

SPAGeDi offers a lot of flexibility in how data files are formatted. read.SPAGeDi accomodates most of that flexibility. The primary exception is that alleles must be delimited in the same way across all genotypes, as specified by allelesep. Comment lines beginning with //, as well as blank lines, are ignored by read.SPAGeDi just as they are by SPAGeDi. read.SPAGeDi is not designed to read dominant data (see section 3.2.2 of the SPAGeDi 1.3 manual). However, see dominant.to.codominant for a way to read this type of data after some simple manipulation in a spreadsheet program. The first line of a SPAGeDi file contains information that is used by read.SPAGeDi. The ploidy as specified in the 6th position of the first line is ignored, and is instead calculated by counting alleles for each individual (including zeros on the right, but not the left, side of the genotype). The number of digits specified in the 5th position of the first line is only used if allelesep="". All other values in the first line are important for the function. If the only alleles found for a particular individual and locus are zeros, the genotype is interpreted as missing. Otherwise, zeros on the left side of a genotype are ignored, and zeros on the right side of a genotype are used in calculating the ploidy but are not included in the genotype object that is returned. If allelesep="", read.SPAGeDi checks that the number of characters in the genotype can be evenly divided by the number of digits per allele. If not, zeros are added to the left of the genotype string before splitting it into alleles.

References

http://ebe.ulb.ac.be/ebe/Software_files/manual_SPAGeDi_1-3.pdf Hardy, O. J. and Vekemans, X. (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2, 618-620.

See Also

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

Examples

# create a file to read (usually done with spreadsheet software or a
# text editor):
cat("// here's a comment line at the beginning of the file",
"5t0t-2t2t2t4",
"4t5t10t50t100",
"IndtLattLongtloc1tloc2",
"ind1t39.5t-120.8t00003133t00004040",
"ind2t39.5t-120.8t3537t4246",
"ind3t42.6t-121.1t5083332t40414500",
"ind4t38.2t-120.3t00000000t41430000",
"ind5t38.2t-120.3t00053137t00414200",
"END",
sep="", file="SpagInputExample.txt")

# display the file
cat(readLines("SpagInputExample.txt"), sep="")

# read the file
mydata <- read.SPAGeDi("SpagInputExample.txt", allelesep = "",
returncatspatcoord = TRUE, returnploidies = TRUE)

# view the data
mydata

# view genotypes by locus
mydata$Genotypes[,"loc1"]
mydata$Genotypes[,"loc2"]