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Plink

plink(infile::String; keepfields::Symbol|Vector{Symbol}, silent::Bool)

Read a PLINK .ped or binary .bed file into memory as a PopData object. Requires an accompanying .fam file in the same directory, but an accompanying .bim file is optional.

  • infile::String : path to .ped or .bed file

Keyword Arguments​

  • famfields::Symbol|Vector{Symbol}: which additional fields to import from the .fam file
    • :all (default)
    • :none
    • any one or combination of [:sire, :dam, :sex, :phenotype]
  • bimfields::Symbol|Vector{Symbol}: which additional fields to import from the optional .bim file
    • :all (default)
    • :none
    • any one or combination of [:chromosome, :cm, :bp]
  • silent::Bool: whether to print file information during import (default: false)

Example

# assumes there is parakeet.ped + parakeet.fam in same directory
julia> parakeet = plink("datadir/parakeet.ped", famfields = :sex)

# assumes there is parrot.ped + parrot.fam in same directory
julia> parrot = plink("datadir/parrot.bed", famfields = [:sire, :dam], bimfields = :chromosome)
plink(data::PopData; filename::String)

Write a biallelic PopData object to PLINK .ped format with an accompanying .fam file. Genotypes are coded by the PLINK standard:

  • Integers are the alleles
  • 0 encodes missing
  • After column 6, every two numbers indicate a diploid genotype such that:
    • 00 Homozygous for first allele
    • 01 Missing genotype
    • 10 Heterozygous
    • 11 Homozygous for second allele

Example

julia> sharks = dropmultiallelic(@gulfsharks) ;
julia> plink(sharks, filename = "biallelic_sharks.ped")