read.SPAGeDi: Read Genotypes in SPAGeDi Format

In polysat: Tools for Polyploid Microsatellite Analysis

Read Genotypes in SPAGeDi Format

Description

read.SPAGeDi can read a text file formatted for the SPAGeDi software and return a genambig object, as well as optionally returning a data frame of spatial coordinates. The genambig object includes genotypes, ploidies, and population identities (from the category column, if present) from the file.

Usage

read.SPAGeDi(infile, allelesep = "/", returnspatcoord = FALSE)

Arguments

infile	A character string indicating the 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 "/", " ", ", ", ".", and "--".
returnspatcoord	Boolean. Indicates whether a data frame should be returned containing the spatial coordinates columns.

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 genbinary.to.genambig 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.

The Ploidies slot of the "genambig" object that is created is initially indexed by both sample and locus, with ploidy being written to the slot on a per-genotype basis. After all genotypes have been imported, reformatPloidies is used to convert Ploidies to the simplest possible format before the object is returned.

Value

Under the default where returnspatcoord=FALSE, a genambig object is returned. Alleles are formatted as integers. The Ploidies slot is filled in according to the number of alleles per genotype, ignoring zeros on the left. If the first line of the file indicates that there are more than zero categories, the category column is used to fill in the PopNames and PopInfo slots.

Otherwise, a list is returned:

SpatCoord	A data frame of 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.
Dataset	A genambig object as described above.

Author(s)

Lindsay V. Clark

References

https://ebe.ulb.ac.be/ebe/SPAGeDi.html

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, genbinary.to.genambig, read.table, read.GeneMapper, read.GenoDive, read.Structure, read.ATetra, read.Tetrasat, read.POPDIST, read.STRand

Examples

# create a file to read (usually done with spreadsheet software or a
# text editor):
myfile <- tempfile()
cat("// here's a comment line at the beginning of the file",
"5\t0\t-2\t2\t2\t4",
"4\t5\t10\t50\t100",
"Ind\tLat\tLong\tloc1\tloc2",
"ind1\t39.5\t-120.8\t00003133\t00004040",
"ind2\t39.5\t-120.8\t3537\t4246",
"ind3\t42.6\t-121.1\t5083332\t40414500",
"ind4\t38.2\t-120.3\t00000000\t41430000",
"ind5\t38.2\t-120.3\t00053137\t00414200",
"END",
sep="\n", file=myfile)

# display the file
cat(readLines(myfile), sep="\n")

# read the file
mydata <- read.SPAGeDi(myfile, allelesep = "",
returnspatcoord = TRUE)

# view the data
mydata
viewGenotypes(mydata[[2]])

polysat documentation built on Aug. 23, 2022, 5:07 p.m.