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Build Genome

build_genome() defines the genetic information including numbers of chromosomes and loci, genetic position, physical position, minor allele frequency, mutation rates, and genotyping error rates.

Quick Start

Quick setup by assigning number of markers and chromosomes.

build_genome(;n_loci ::Int64=-1,
              n_chr    ::Int64=10,
              species  ::String="none",
              args...)

Arguments

  • n_loci : Number of simulated markers for each chromosome
  • n_chr: Number of simulated chromosome with length of 100 centimorgan
  • species : Infer genetic position (Morgan) by pre-load linkage maps. Available species are: ['pig', 'cattle', 'maize', 'rice'].

Examples

julia> build_genome(n_chr    = 2,
                    n_loci = 10000)

[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome  : 2
[ Info:
[ Info: Chromosome Length (cM): 200.0
[ Info: [100.0, 100.0]
[ Info:
[ Info: Number of Loci        : 20000
[ Info: [10000, 10000]
[ Info:
[ Info: Genotyping Error      : 0.0
[ Info: Mutation Rate         : 0.0
[ Info:

Build by a File or a DataFrame

Define genome by providing a formatted dataframe or a path to the file.

build_genome(dt      ::DataFrame;
             species ::String="none",
             args...)

build_genome(filename::String;
             species ::String="none",
             args...)

Arguments

  • dt : A DataFrame with required columns of chr and cM, or chr and bp if species is provided for the inference.
  • filename : A filepath to the file containing genome information.
  • species : Adjust genetic position (Morgan) by pre-load linkage maps, available species are: ["cattle", and "pig"]

Example of the DataFrame

4×7 DataFrame
 Row │ id      chr    bp       cM       MAF      eff_1    eff_2
     │ String  Int64  Int64    Float64  Float64  Float64  Float64
─────┼────────────────────────────────────────────────────────────
   1 │ snp_1       1  1818249     50.8      0.5      0.1      0.0
   2 │ snp_2       1  6557697     80.3      0.5      0.0      0.0
   3 │ snp_3       2  2298800     39.2      0.5      0.2      0.0
   4 │ snp_4       2  5015698     66.3      0.5      0.0      0.5

Examples

The preloaded file can be located through:

# Filepath to the preloaded map file
julia> filepath = PATH("map")

Build genome by a filepath

julia> build_genome(filepath;
                    rate_mutation=0.005, rate_error=0.01)

or by a dataframe

julia> using DataFrames
julia> data = CSV.read(filepath, DataFrame)
julia> build_genome(data;
                    rate_mutation=0.005, rate_error=0.01)

[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome  : 2
[ Info:
[ Info: Chromosome Length (cM): 146.6
[ Info: [80.3, 66.3]
[ Info:
[ Info: Number of Loci        : 4
[ Info: [2, 2]
[ Info:
[ Info: Genotyping Error      : 0.01
[ Info: Mutation Rate         : 0.005
[ Info:

Use cattle genome as reference to infer the genetic positions

julia> build_genome(filepath; species="cattle")

[ Info: Arias,J.A. et al. (2009) A high density linkage map of the bovine genome. BMC Genetics, 10, 18.
[ Info: Reference Genome : Btau 4.0
[ Info: SNP Chip         : Affymetrix GeneChip Bovine Mapping 10K SNP kit

┌ Warning: The provided genetic distances will be replaced with ones infered from preloaded linkage maps
└ @ XSim ~/Dropbox/projects/XSim/src/objects/global.jl:118
[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome  : 2
[ Info:
[ Info: Chromosome Length (cM): 16.8
[ Info: [15.1, 1.7]
[ Info:
[ Info: Number of Loci        : 4
[ Info: [2, 2]
[ Info:
[ Info: Genotyping Error      : 0.0
[ Info: Mutation Rate         : 0.0
[ Info:

Build by Pre-Loaded Genome

Define genome by pre-loaded genome from reference.

build_genome(;species :: String="none")

Arguments

  • species : Adjust genetic position (Morgan) by pre-load linkage maps, available species are: ["cattle", and "pig"]

Examples

julia> build_genome(species="pig")
[ Info: Tortereau,F. et al. (2012) A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics, 13, 586.
[ Info: Reference Genome : Sscrofa 10.2
[ Info: SNP Chip         : PorcineSNP60 BeadChip
[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome  : 18
[ Info: 
[ Info: Chromosome Length (cM):
[ Info: [98.0, 94.7, 96.8, 92.2, 89.3, 124.1, 112.8, 94.8, 95.4, 84.4, 64.6, 77.0, 97.6, 106.6, 93.5, 66.5, 53.9, 49.1]
[ Info: 
[ Info: Number of Loci        : 45292
[ Info: [6580, 2356, 1938, 3682, 2217, 1766, 3489, 2100, 2538, 1281, 1805, 1072, 3529, 4053, 2612, 1513, 1646, 1115]
[ Info: 
[ Info: Genotyping Error      : 0.0
[ Info: Mutation Rate         : 0.0
[ Info:

Build by Explicit Definition

Define genome by providing genetic information of each loci explicitly.

build_genome(chromosome    ::Array{Int64,   1},
             bp            ::Array{Int64,   1},
             cM            ::Array{Float64, 1},
             maf           ::Array{Float64, 1};
             rate_mutation ::Float64=0.0,
             rate_error    ::Float64=0.0)

Arguments

  • chromosome : Chromosome codes
  • bp : Physical positions
  • cM : Genetic positions
  • maf : Minor allele frequencies
  • rate_mutation : Mutation rate
  • rate_error : Error rate of genotyping

Examples

julia> ch  = [1,    1,     2,    2,    2]
julia> bp  = [130,  205,   186,  503,  780]
julia> cM  = [85.7, 149.1, 37.4, 83.6, 134.3]
julia> maf = [0.5,  0.5,   0.5,  0.5,  0.5]
julia> build_genome(ch, bp, cM, maf)

[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome  : 2
[ Info:
[ Info: Chromosome Length (cM): 283.4
[ Info: [149.1, 134.3]
[ Info:
[ Info: Number of Loci        : 5
[ Info: [2, 3]
[ Info:
[ Info: Genotyping Error      : 0.0
[ Info: Mutation Rate         : 0.0
[ Info: