Read genotypes from a file — read

Reads the common population genetic file formats into a popcounts object (allele counts per population and locus), which is what pairwise_fst() and directional_gst() use.

Usage

read_genotypes(
  file,
  format = c("auto", "structure", "genepop", "vcf", "genalex", "fstat", "plink"),
  pop = NULL,
  missing = c("-9"),
  onerowperind = NULL,
  label = NULL,
  popdata = NULL,
  popflag = FALSE,
  locdata = FALSE,
  phenotype = FALSE,
  extracols = 0,
  pop_names = NULL
)

Arguments

file: Path to the genotype file.
format: One of "auto" (guess from the extension), "structure", "genepop", "vcf", "genalex", "fstat", "plink".
pop: Optional population assignment that overrides the one in the file: a vector with one value per individual in file order, a two-column data.frame or whitespace-separated file (individual, population), or a function that takes individual names and returns populations (for example function(x) sub("_.*", "", x)).
missing: STRUCTURE only: codes for missing alleles.
onerowperind, label, popdata, popflag, locdata, phenotype, extracols: STRUCTURE only. NULL means detect: the row layout is detected from repeated labels, and the leading columns from the marker-name row when there is one. Otherwise the defaults are a label and a population column, which is the most common layout.
pop_names: GENEPOP only: names for the populations, in file order. By default each population takes the name of its first individual, which is the GENEPOP convention.

Value

A popcounts object.

Supported formats

STRUCTURE (.str, .stru, .structure): Both layouts: one row per individual (two columns per locus) or two rows per individual (one column per locus). Optional leading columns, in STRUCTURE's order: a label, the population (POPDATA), POPFLAG, LOCDATA, PHENOTYPE and any extra columns. An optional first row of marker names is detected automatically. Alleles may be any integer codes; missing data are -9 by default. When the file has a marker-name row, the number of leading columns is worked out from it, otherwise set the arguments below.
GENEPOP (.gen, .genepop): Title line, loci one per line or comma-separated, Pop separators, and name , genotypes rows. Two- or three-digit allele codes (detected from the genotype width), haploid or diploid; 0, 00, 000 and so on are missing.
VCF (.vcf, .vcf.gz): Any ploidy, phased or unphased, biallelic or multiallelic. VCF has no populations, so supply pop.
GenAlEx (.csv): The standard codominant layout: a first row with the number of loci, individuals and populations, a second row with population names, a header row, then sample, population and two columns per locus.
FSTAT (.dat): The standard header (populations, loci, maximum allele, digits per allele), locus names, then population and genotype columns.
PLINK (.ped with .map, or .raw from --recode A): The family ID is used as the population unless pop is given. Convert binary .bed files with plink --recode A or to VCF first.

Objects already in R (adegenet genind, genpop, genlight, or a vcfR object) go through as_popcounts() instead.

Examples

ex <- corridor_example()
read_genotypes(ex$files$structure)
#> <popcounts> 80 populations, 1318 loci (2 alleles per locus)
#>   individuals per population: 8-8
#>   populations: M01, M02, M03, M04, M05, M06, M07, M08 ... 
# \donttest{
read_genotypes(ex$files$genepop)
#> <popcounts> 80 populations, 1318 loci (2 alleles per locus)
#>   individuals per population: 8-8
#>   populations: M01_01, M02_01, M03_01, M04_01, M05_01, M06_01, M07_01, M08_01 ... 
read_genotypes(ex$files$vcf, pop = ex$files$popmap)
#> <popcounts> 80 populations, 1318 loci (2 alleles per locus)
#>   individuals per population: 8-8
#>   populations: M01, M02, M03, M04, M05, M06, M07, M08 ... 
# }