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PopData.jl

PopGenCore.jl/src/PopData.jl​

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

🟪🔵 PopObj​

PopObj::AbstractType

Generic AbstractType for use in PopGen.jl

🟪🔵 PopDataInfo​

mutable struct PopDataInfo
    samples::Int64
    sampeinfo::DataFrame
    loci::Int64
    locusinfo::DataFrame
    populations::Int64
    ploidy::Union{Int8, Vector{Int8}}
    biallelic::Bool
end

The data struct used internally as PopData.metadata fields to store basic information about the PopData for easy access.

PopDataInfo(genodf::DataFrame)

constructor format using just the genodata dataframe

🟪🔵 PopData​

PopData
    metadata::PopDataInfo
    genodata::DataFrame

The data struct used for the PopGen population genetics ecosystem. You are strongly discouraged from manually creating tables to pass into a PopData, and instead should use the provided file importers and utilities.

- `metadata` PopDataInfo of  data information
    - `samples` - the number of samples in the data
    - `sampleinfo` - DataFrame of sample names,populations, ploidy, etc.
    - `loci` - the number of loci in the data
    - `locusinfo` - DataFrame of locus names, chromosome, physical position, etc.
    - `populations` - the number of populations in the data
    - `ploidy` - the ploidy (or ploidies) present in the data
    - `biallelic` - if all the markers are biallelic
- `genodata` DataFrame of sample genotype records
    - `name` - the individual/sample names [`PooledArray`]
    - `population` - population names [`PooledArray`]
    - `locus` - locus names [`PooledArray`]
    - `genotype` - genotype values [`NTuple{N,Signed}`]

PopData(data::DataFrame) Contructor using just a genodata dataframe.

🟪🔵 PopDataInfo!​

PopDataInfo!(data::PopData)

This method is used to update PopDataInfo from PopData, all in one swoop

PopDataInfo!(popdatainfo::PopDataInfo, genodata::DataFrame)

Method to update preexisting PopDataInfo with new genodata, useful for getindex and creating new PopData from that

🟪🔵 Genotype​

Genotype::DataType

For convenience purposes, an alias for NTuple{N, <:Signed} where N, which is the type describing individual genotypes in PopData. Specifically, there exist SNP as an alias for NTuple{N, Int8} and MSat for NTuple{N, Int16}

🟪🔵 SNP​

SNP::DataType

An alias for NTuple{N, Int8}

📦 _SNP​

SNP(geno)

Contstructor for SNP

🟪🔵 MSat​

MSat::DataType

An alias for NTuple{N, Int16}

📦 _MSat​

_MSat(geno)

Constructor for MSat

🟪🔵 GenoArray​

GenoArray::DataType

An alias for an AbstractVector of elements Missing and Genotype, which itself is of type NTuple{N, <:Integer} where N. The definition as an AbstractVector adds flexibility for SubArray cases.

📦 _ploidy2text​

_ploidy2text(ploidy::Int8)
_ploidy2text(ploidy::Vector{Int8})

🟪🔵 Base.show​

Base.show(io::IO, data::PopData)
Base.show(io::IO, data::PopDataInfo)

🟪🔵 Base.getindex​

Base.getindex(data::PopData, idx::Symbol)
Base.getindex(data::PopData, args)
Base.getindex(data::PopData, expression, cols)

🟪🔵 Base.getproperty​

getproperty(data::PopData, field::Symbol)

A convenience method to access certain elements in a PopData with fewer keystrokes. Essentially a standard getproperty call, except sampleinfo accesses metadata.sampleinfo, locusinfo accesses metadata.locusinfo, and info is an alias for metadata.

Example

cats = @nancycats ;
cats.metadata == cats.info
cats.metadata.sampleinfo == cats.sampleinfo
cats.metadata.locusinfo == cats.locusinfo