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Plink.jl

PopGenCore.jl/src/io/Plink.jl​

📦 not exported🟪 exported by PopGenCore.jl🔵 exported by PopGen.jl

📦 _plinkindex​

_plinkindex(s::Matrix{UInt8}, i::Integer, j::Integer)
_plinkindex(s::Matrix{UInt8})

Tthis function copies the getindex tool OpenMendel/SnpArrays.jl uses to pull out the byte values from the compressed hex genotypes Repo: https://github.com/OpenMendel/SnpArrays.jl

📦 _SNP​

_SNP(genotype::UInt8)
_SNP(genomatrix::AbstractArray{UInt8})
  • 00 Homozygous for first allele (0x00)
  • 01 Missing genotype (0x01)
  • 10 Heterozygous (0x02)
  • 11 Homozygous for second allele in .bim file (0x03)

📦 _plinkped​

_plinkped(infile::String, keepfields::Union{Symbol,Vector{Symbol}} = :all, silent::Bool = false)

📦 _plinkbed​

_plinkbed(infile::String, famfields::Union{Symbol,Vector{Symbol}} = :all, bimfields::Union{Symbol,Vector{Symbol}} = :all, silent::Bool = false)

📦 _genoconversion​

_genoconversion(genotype::T) where T<:Genotype = join(genotype, " ")
_genoconversion(genotype::Missing) = "0 0"

🟪🔵 plink​

plink(infile::String; famfields::Union{Symbol,Vector{Symbol}} = :all, bimfields::Union{Symbol,Vector{Symbol}} = :all, silent::Bool = false)

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​

parakeet = plink("datadir/parakeet.ped", famfields = :sex)
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.

Example​

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