build_genome(species="cattle")
[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome : 29
[ Info:
[ Info: Chromosome Length (cM): 3076.0
[ Info: [166.0, 144.0, 142.0, 133.0, 122.0, 134.0, 126.0, 123.0, 110.0, 119.0, 130.0, 117.0, 118.0, 127.0, 108.0, 112.0, 97.0, 103.0, 99.0, 74.0, 88.0, 91.0, 90.0, 86.0, 62.0, 70.0, 61.0, 57.0, 67.0]
[ Info:
[ Info: Number of Loci : 6231
[ Info: [370, 296, 295, 277, 292, 283, 253, 258, 210, 261, 283, 220, 255, 205, 214, 217, 209, 172, 154, 210, 137, 190, 155, 186, 106, 145, 116, 137, 125]
[ Info:
[ Info: Genotyping Error : 0.0
[ Info: Mutation Rate : 0.0
[ Info:
[ 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
reference = XSim.data("cattle_map") first(reference, 5)
5×4 DataFrame
Row │ id chr bp cM
│ String Int64 Int64 Float64
─────┼──────────────────────────────────────
1 │ ALGA0000112 1 1276597 0.033
2 │ ALGA0000120 1 1352912 0.033
3 │ ALGA0000131 1 1461555 0.033
4 │ ALGA0000133 1 1486605 0.033
5 │ ALGA0000134 1 1519802 0.033
build_genome(reference)
[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome : 18
[ Info:
[ Info: Chromosome Length (cM): 1591.0
[ Info: [98.0, 95.0, 97.0, 92.0, 89.0, 124.0, 113.0, 95.0, 95.0, 84.0, 65.0, 77.0, 98.0, 107.0, 93.0, 66.0, 54.0, 49.0]
[ 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:
n_chr = 2 n_loci_chr = 5 n_loci = n_chr * n_loci_chr chromosome = [i for i in 1:n_chr for j in 1:n_loci_chr] bp = [10 * j for i in 1:n_chr for j in 1:n_loci_chr] cM = [1.5 * j for i in 1:n_chr for j in 1:n_loci_chr] maf = fill(0.5, n_loci) rate_mutation = 0.0 rate_error = 0.0 build_genome(chromosome, bp, cM, maf, rate_mutation, rate_error)
[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome : 2
[ Info:
[ Info: Chromosome Length (cM): 16.0
[ Info: [8.0, 8.0]
[ Info:
[ Info: Number of Loci : 10
[ Info: [5, 5]
[ Info:
[ Info: Genotyping Error : 0.0
[ Info: Mutation Rate : 0.0
[ Info:
n_qtl = [2, 2] Vg = [ 1 .6 .5 1] build_phenome(n_qtl, Vg)
[ Info: --------- Phenome Summary ---------
[ Info: Number of Traits : 2
┌ Info:
│ Genetic_Variance =
│ 2×2 Array{Float64,2}:
│ 1.0 0.6
└ 0.6 1.0
[ Info: Number of QTLs : [2 3]
effects = Array([0 0 0 .5 0 .3 0 0 0 0 .3 0 0 0 .8 0 0 .1 0 0]') Vg = [ 1 .5 .5 1] build_phenome(effects, Vg)
[ Info: --------- Phenome Summary ---------
[ Info: Number of Traits : 2
┌ Info:
│ Genetic_Variance =
│ 2×2 Array{Float64,2}:
│ 1.0 0.5
└ 0.5 1.0
[ Info: Number of QTLs : [2 5]
build_demo()
[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome : 10
[ Info:
[ Info: Chromosome Length (cM): 1500.0
[ Info: [150.0, 150.0, 150.0, 150.0, 150.0, 150.0, 150.0, 150.0, 150.0, 150.0]
[ Info:
[ Info: Number of Loci : 1000
[ Info: [100, 100, 100, 100, 100, 100, 100, 100, 100, 100]
[ Info:
[ Info: Genotyping Error : 0.0
[ Info: Mutation Rate : 0.0
[ Info:
[ Info: --------- Phenome Summary ---------
[ Info: Number of Traits : 2
┌ Info:
│ Genetic_Variance =
│ 2×2 Array{Float64,2}:
│ 1.0 0.0
└ 0.0 1.0
[ Info: Number of QTLs : [3 8]
build_demo_small()
[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome : 2
[ Info:
[ Info: Chromosome Length (cM): 16.0
[ Info: [8.0, 8.0]
[ Info:
[ Info: Number of Loci : 10
[ Info: [5, 5]
[ Info:
[ Info: Genotyping Error : 0.0
[ Info: Mutation Rate : 0.0
[ Info:
[ Info: --------- Phenome Summary ---------
[ Info: Number of Traits : 2
┌ Info:
│ Genetic_Variance =
│ 2×2 Array{Float64,2}:
│ 1.0 0.0
└ 0.0 1.0
[ Info: Number of QTLs : [2 4]
You can always check the settings with summary()
function
summary()
[ Info: --------- Genome Summary ---------
[ Info: Number of Chromosome : 10
[ Info:
[ Info: Chromosome Length (cM): 1500.0
[ Info: [150.0, 150.0, 150.0, 150.0, 150.0, 150.0, 150.0, 150.0, 150.0, 150.0]
[ Info:
[ Info: Number of Loci : 1000
[ Info: [100, 100, 100, 100, 100, 100, 100, 100, 100, 100]
[ Info:
[ Info: Genotyping Error : 0.0
[ Info: Mutation Rate : 0.0
[ Info:
[ Info: --------- Phenome Summary ---------
[ Info: Number of Traits : 2
┌ Info:
│ Genetic_Variance =
│ 2×2 Array{Float64,2}:
│ 1.0 0.0
└ 0.0 1.0
[ Info: Number of QTLs : [3 8]