AlleleMatrices.jl

PopGenCore.jl/src/AlleleMatrices.jl

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

🟪 matrix

matrix(data::PopData, matrixtype::String = "frequency"; missings = "mean", scale = false, center = false)

Return a matrix of allele counts or frequencies per genotype where rows are samples and columns are the occurence count or frequency of an allele for that locus in that sample. Loci and alleles are sorted alphanumerically. The scale and center keywords are only relevant for allele frequencies, not counts.

Positional Arguments

data: a PopData object
matrixtype: a String or Symbol of count or frequency (default: frequency)

Keyword Arguments

missings: a String denoting how to handle missing values when outputting frequency (default: mean)
- "missing": fallback method to keep missing values as they are
- "zero": replace missing values with 0
- "mean": replace missing values with the mean frequency for that allele in that locus
scale: a 'Bool' of whether to z-score scale allele frequencies (default: false)
center: a Bool of whether to center the allele frequencies (default: 'false')

Example

julia> cats = @nancycats ;
julia> cnts = matrix(cats, "count") ;  cnts[1:5,1:6]
5×6 Matrix{Union{Missing, Int8}}:
  missing   missing   missing   missing   missing   missing
  missing   missing   missing   missing   missing   missing
 0         0         0         0         0         0
 0         0         0         0         0         0
 0         0         0         0         0         0

julia> frq = matrix(cats, "frequency") ;  frq[1:5,1:6]
5×6 Matrix{Union{Missing, Float32}}:
 0.00460829  0.00460829  0.0276498  0.133641  0.00460829  0.0921659
 0.00460829  0.00460829  0.0276498  0.133641  0.00460829  0.0921659
 0.0         0.0         0.0        0.0       0.0         0.0
 0.0         0.0         0.0        0.0       0.0         0.0
 0.0         0.0         0.0        0.0       0.0         0.0

julia> frq = matrix(cats, :frequency, missings = "zero") ;  frq[1:5,1:6]
 5×6 Matrix{Float64}:
 0.0  0.0  0.0  0.0  0.0  0.0
 0.0  0.0  0.0  0.0  0.0  0.0
 0.0  0.0  0.0  0.0  0.0  0.0
 0.0  0.0  0.0  0.0  0.0  0.0
 0.0  0.0  0.0  0.0  0.0  0.0
 
 julia> frq = matrix(cats, missings = "mean", scale = true, center = true) ;  frq[1:5,1:6]
 5×6 Matrix{Float32}:
  7.17017f-9   7.17017f-9   0.0        0.0        7.17017f-9   0.0
  7.17017f-9   7.17017f-9   0.0        0.0        7.17017f-9   0.0
 -0.0709577   -0.0709577   -0.175857  -0.394198  -0.0709577   -0.300797
 -0.0709577   -0.0709577   -0.175857  -0.394198  -0.0709577   -0.300797
 -0.07

📦 _setcounts

📦 _matrix

_matrix(data::PopData, ::Val{:count})

Create a matrix of allele count per genotype where rows are samples and columns are the occurence count of an allele for that locus in that sample. Missing values are preserved as -1.

_matrix(data::PopData, ::Val{:frequencyzero})

Create a matrix of allele frequencies per genotype where rows are samples and columns are the frequency of an allele for that locus in that sample. Missing values are replaced by zeros.

_matrix(data::PopData, ::Val{:frequencymean})

Create a matrix of allele frequencies per genotype where rows are samples and columns are the frequency of an allele for that locus in that sample. Missing values are replaced by the global mean allele frequency.

_matrix(data::PopData, ::Val{:frequencymissing})

Create a matrix of allele frequencies per genotype where rows are samples and columns are the frequency of an allele for that locus in that sample. Missing values are kept as missing.

🟪 featurematrix

featurematrix(data::PopData, matrixtype::Union{String, Symbol} = "genotype")

Positional Arguments

- `data`: a PopData object
- `matrixtype`: a `String` or `Symbol` of `genotype`, or `allele` (default: `genotype`)

genotype feature matrix

Return a matrix of dummy-encoded genotypes (0,1,2...), where rows correspond with samples and columns correspond to loci. Missing genotypes are encoded as -1. For biallelic loci, 0 encodes homozygous for allele 1, 1 encodes for a heterozygote, and 2 encodes for homozygous allele 2.

allele feature matrix

Return a matrix of dummy-encoded alleles (0,1), where rows correspond with samples and columns correspond to alleles within loci, such that there are as many columns per locus as alleles for that locus. Missing alleles (from missing genotypes) are encoded as -1.

Example

julia> cats = @nancycats ;
julia> featurematrix(cats)
237×9 Matrix{Int8}:
 -1   0   0   0   0  0   0   0   0
 -1   1   1   1   0  0   1   0   0
  0   0   2   2   1  1   2   0   1
  1   2   3   3   2  0   0   1   0
  1   3   4   4   3  0   3   0   0
  ⋮                  ⋮
 49   0   1  -1  36  0   0  -1  13
 48   6   8  -1  25  1   2  -1   0
 29   9  23  -1   7  3  26  14   0
  3   5   8  -1   2  1   3  14   0
 29  10  16  -1   4  3   2  -1   0

julia> featurematrix(cats, "allele")
237×108 Matrix{Int8}:
 -1  -1  -1  -1  -1  …  0  0  0  0  0  0
 -1  -1  -1  -1  -1     0  0  0  0  0  0
  0   0   0   0   0     0  0  0  0  0  0
  0   0   0   0   0     0  0  0  0  0  0
  0   0   0   0   0     0  0  0  0  0  0
  ⋮                  ⋱           ⋮
  0   0   0   0   0     0  0  0  1  0  0
  0   0   0   0   0     0  0  0  0  0  0
  0   0   0   0   0     0  0  0  0  0  0
  0   0   0   0   0  …  0  0  0  0  0  0
  0   0   0   0   0     0  0  0  0  0  0 

_featurematrix(data::PopData, ::Val{:genotype})

_featurematrix(data::PopData, ::Val{:allele})

Return a matrix of dummy-encoded alleles (0,1,2...), where rows correspond with samples and columns correspond to loci. Missing genotypes are encoded as -1.

PopGenCore.jl/src/AlleleMatrices.jl​

🟪 matrix​

📦 _setcounts​

📦 _matrix​

🟪 featurematrix​

PopGenCore.jl/src/AlleleMatrices.jl

🟪 matrix

📦 _setcounts

📦 _matrix

🟪 featurematrix