This folder contain example data to run this engine.
Genetic data.
The .vcf files are not “gitted”.
list.files("geno")
#> [1] "breedGame_geno.vcf.gz" "testMarkerData01.vcf"
#> [3] "testMarkerData01.vcf.gz"cat(paste(readLines("geno/testMarkerData01.vcf", n=20), collapse = "\n"))
#> ##fileformat=VCFv4.2
#> ##fileDate=20160228
#> ##source=PLINKv1.90
#> ##contig=<ID=1,length=43269459>
#> ##contig=<ID=2,length=35935336>
#> ##contig=<ID=3,length=36413110>
#> ##contig=<ID=4,length=35462739>
#> ##contig=<ID=5,length=29945612>
#> ##contig=<ID=6,length=31247344>
#> ##contig=<ID=7,length=29693501>
#> ##contig=<ID=8,length=28441873>
#> ##contig=<ID=9,length=22974049>
#> ##contig=<ID=10,length=23205939>
#> ##contig=<ID=11,length=29020004>
#> ##contig=<ID=12,length=27530631>
#> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] SONA_CHUR::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] KIRIMINY::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] ZABI::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] KAUKHNYIN_ANI::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] KUNING::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] SABA::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] TUMO_TUMO::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] D_2-22::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] VAZAKONANDRIANA::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] KULING::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] ARC_12429::[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
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list.files("pheno")
#> [1] "breedGame_pheno.csv" "testPhenoData01.csv"cat(paste(readLines("pheno/testPhenoData01.csv", n=10), collapse = "\n"))
#> ,Flowering.time.at.Arkansas,Flowering.time.at.Faridpur,Flowering.time.at.Aberdeen,FT.ratio.of.Arkansas.Aberdeen,FT.ratio.of.Faridpur.Aberdeen,Culm.habit,Leaf.pubescence,Flag.leaf.length,Flag.leaf.width,Awn.presence,Panicle.number.per.plant,Plant.height,Panicle.length,Primary.panicle.branch.number,Seed.number.per.panicle,Florets.per.panicle,Panicle.fertility,Seed.length,Seed.width,Seed.volume,Seed.surface.area,Brown.rice.seed.length,Brown.rice.seed.width,Brown.rice.surface.area,Brown.rice.volume,Seed.length.width.ratio,Brown.rice.length.width.ratio,Seed.color,Pericarp.color,Straighthead.suseptability,Blast.resistance,Amylose.content,Alkali.spreading.value,Protein.content,Year07Flowering.time.at.Arkansas,Year06Flowering.time.at.Arkansas
#> [email protected],75.08333333,64,81,0.926954733,0.790123457,4,1,28.375,1.283333333,0,3.068052935,110.9166667,20.48181818,9.272727273,4.785975442,4.914658225,0.879,8.064116667,3.685183333,2.587447569,3.914120138,5.794541667,3.113958333,3.51115158,7.737358333,2.188,1.861,0,0,4.833333334,8,15.61333333,6.083333334,8.45,73,77.16666667
#> [email protected],89.5,66,83,1.078313253,0.795180723,7.5,0,39.00833333,1,0,4.051784948,143.5,26.83333333,9.166666667,4.439705746,4.727387819,0.75,7.705383333,2.951458333,2.111145089,3.658708865,5.603658333,2.56645,3.287373062,5.10535,2.611,2.183,0,0,7.831666667,4,23.26,5.638888889,9.2,88,91
#> [email protected],94.5,67,93,1.016129032,0.720430108,6,1,27.68333333,1.516666667,0,3.124565145,128.0833333,23.53333333,8.666666667,5.07970897,5.146436835,0.935,8.237575,2.926366667,2.154758678,3.713855969,6.120341667,2.466983333,3.334125877,5.126958333,2.815,2.481,0,0,NA,3,23.12,5.527777778,8,105.5,83.5
#> [email protected],87.5,70,108,0.810185185,0.648148148,3.5,1,30.41666667,0.891666667,0,3.697178257,153.75,28.96363636,6.363636364,4.523960131,4.730921391,0.813,9.709375,2.3821,1.94022138,3.700053664,7.089883333,2.044608333,3.297791744,4.085133333,4.076,3.468,0,0,8.333333334,5,19.32333333,6.027777778,9.6,86.5,88.5
#> [email protected],89.08333333,73,101,0.882013201,0.722772277,6,1,36.90833333,1.75,0,2.857427602,148.3333333,30.91666667,11.16666667,5.538645743,5.676468373,0.871,7.118183333,3.281891667,2.202359519,3.657370297,5.136483333,2.803858333,3.284327991,5.555183333,2.169,1.832,0,0,8.166666667,3,23.24,5.444444445,8.5,85.5,92.66666667
#> [email protected],105,NA,158,0.664556962,NA,3,1,36.99,1.55,1,2.859021228,119.6,24.625,13.33333333,5.338018733,5.43590303,0.907,7.347254545,2.528890909,1.774465329,3.474791087,5.485345455,2.188881818,3.101568676,3.591045455,2.905,2.506,0,0,8.585,2,20.18666667,6,11.75,105,NA
#> [email protected],101.5833333,74,122,0.832650273,0.606557377,2.5,NA,41.95,1.858333333,0,2.621038824,147.4166667,31.5,12.22222222,5.54691205,5.794705943,0.781,8.572091667,2.654675,2.044537332,3.691182217,6.510433333,2.241341667,3.304196579,4.524383333,3.229,2.905,0,0,6.998333334,2,22.195,6.75,8.7,97.5,105.6666667
#> [email protected],73,75,81,0.901234568,0.925925926,6.5,1,24.425,1.2125,1,2.924504764,128.875,20.2,7.875,4.620058798,4.739482524,0.887,7.679875,3.3821875,2.352660146,3.768963219,5.459725,2.917775,3.385437596,6.3641875,2.271,1.871,0,0,7.168333334,9,22.56333333,5.25,9.9,71,79
#> [email protected],89,55,74,1.202702703,0.743243243,3,NA,27.9,1,1,3.650658241,83,22.16666667,10.33333333,4.110873864,4.733270189,0.537,7.859,3.23325,2.265360786,3.729249146,5.088266667,2.937733333,3.309969856,5.9129,2.431,1.732,0,0,3.33,2,15.09666667,7,9.5,89,NAExample of pedigree file. This is fictive pedigree file inspired by Greek mythology. It is the same pedigree in 3 versions:
- Individual name with character string
- Individual name with numbers
- Pedigree with missing founders
cat(paste(readLines("pedigree/testPedData_char.csv", n=10), collapse = "\n"))
#> ind,parent1,parent2
#> Pluto,,
#> Zeus,,
#> Leda,,
#> Dione,,
#> Tantale,Pluto,Zeus
#> Europe,Zeus,Leda
#> Pelos,Dione,Tantale
#> Minos,Zeus,Europe
#> Pelopia,Pelos,PelosTo store the example of results created by the engine.
This can be done automatically using:
createResultExample()list.files("results")
#> [1] "ajdResults.json" "genomicRelationship.csv"
#> [3] "genomicRelationship.json" "gwasResult.json"
#> [5] "ldplot.png" "manplot.html"
#> [7] "manplot.png" "pedigreeNetwork.html"
#> [9] "pedigreeRelationship.csv" "pedigreeRelationship.json"
#> [11] "relationshipHeatmap.html" "relationshipHeatmap.png"cat(paste(readLines("results/gwasResult.json", n=30), collapse = "\n"))
#> {
#> "gwas": [
#> {
#> "chr": "1",
#> "pos": 9563,
#> "id": "SNP-1.8562.",
#> "A1": "A",
#> "A2": "T",
#> "freqA2": 0.135854341736695,
#> "score": 4.39502824590197,
#> "p": 0.036043862635721
#> },
#> {
#> "chr": "1",
#> "pos": 25922,
#> "id": "SNP-1.24921.",
#> "A1": "C",
#> "A2": "T",
#> "freqA2": 0.125352112676056,
#> "score": 1.67445585071392,
#> "p": 0.195662771396972
#> },
#> {
#> "chr": "1",
#> "pos": 26254,
#> "id": "SNP-1.25253.",
#> "A1": "A",
#> "A2": "T",
#> "freqA2": 0.293539325842697,
#> "score": 3.65922266048491,cat(paste(readLines("results/pedigreeRelationship.csv", n=30), collapse = "\n"))
#> #info=R-geno-engine, Pedigree relationship matrix
#> #date=2022-03-11 12:05:27
#> #nInds=20
#> #pedFP=8a6b7f58359f42470000f4a5a2d440d7
#> "Pluto","Zeus","Leda","Dione","Tantale","Europe","Pelos","Minos","Pelopia","Atree","Catree","Egiste","Aerope","Menelas","Agamemnon","Clytemnestre","Helene","Electre","Oreste","Hyphigenie"
#> "Pluto",1,0,0,0,0.5,0,0.25,0,0.25,0.25,0,0.25,0,0.125,0.125,0,0,0.0625,0.0625,0.0625
#> "Zeus",0,1,0,0,0.5,0.5,0.25,0.75,0.25,0.25,0.375,0.25,0.1875,0.21875,0.21875,0.5,0.5,0.359375,0.359375,0.359375
#> "Leda",0,0,1,0,0,0.5,0,0.25,0,0,0.125,0,0.0625,0.03125,0.03125,0.5,0.5,0.265625,0.265625,0.265625
#> "Dione",0,0,0,1,0,0,0.5,0,0.5,0.5,0,0.5,0,0.25,0.25,0,0,0.125,0.125,0.125
#> "Tantale",0.5,0.5,0,0,1,0.25,0.5,0.375,0.5,0.5,0.1875,0.5,0.09375,0.296875,0.296875,0.25,0.25,0.2734375,0.2734375,0.2734375
#> "Europe",0,0.5,0.5,0,0.25,1,0.125,0.75,0.125,0.125,0.375,0.125,0.1875,0.15625,0.15625,0.5,0.5,0.328125,0.328125,0.328125
#> "Pelos",0.25,0.25,0,0.5,0.5,0.125,1,0.1875,1,1,0.09375,1,0.046875,0.5234375,0.5234375,0.125,0.125,0.32421875,0.32421875,0.32421875
#> "Minos",0,0.75,0.25,0,0.375,0.75,0.1875,1.25,0.1875,0.1875,0.625,0.1875,0.3125,0.25,0.25,0.5,0.5,0.375,0.375,0.375
#> "Pelopia",0.25,0.25,0,0.5,0.5,0.125,1,0.1875,1.5,1,0.09375,1.25,0.046875,0.5234375,0.5234375,0.125,0.125,0.32421875,0.32421875,0.32421875
#> "Atree",0.25,0.25,0,0.5,0.5,0.125,1,0.1875,1,1.5,0.09375,1,0.046875,0.7734375,0.7734375,0.125,0.125,0.44921875,0.44921875,0.44921875
#> "Catree",0,0.375,0.125,0,0.1875,0.375,0.09375,0.625,0.09375,0.09375,1,0.09375,0.5,0.296875,0.296875,0.25,0.25,0.2734375,0.2734375,0.2734375
#> "Egiste",0.25,0.25,0,0.5,0.5,0.125,1,0.1875,1.25,1,0.09375,1.5,0.046875,0.5234375,0.5234375,0.125,0.125,0.32421875,0.32421875,0.32421875
#> "Aerope",0,0.1875,0.0625,0,0.09375,0.1875,0.046875,0.3125,0.046875,0.046875,0.5,0.046875,1,0.5234375,0.5234375,0.125,0.125,0.32421875,0.32421875,0.32421875
#> "Menelas",0.125,0.21875,0.03125,0.25,0.296875,0.15625,0.5234375,0.25,0.5234375,0.7734375,0.296875,0.5234375,0.5234375,1.0234375,0.6484375,0.125,0.125,0.38671875,0.38671875,0.38671875
#> "Agamemnon",0.125,0.21875,0.03125,0.25,0.296875,0.15625,0.5234375,0.25,0.5234375,0.7734375,0.296875,0.5234375,0.5234375,0.6484375,1.0234375,0.125,0.125,0.57421875,0.57421875,0.57421875
#> "Clytemnestre",0,0.5,0.5,0,0.25,0.5,0.125,0.5,0.125,0.125,0.25,0.125,0.125,0.125,0.125,1,0.5,0.5625,0.5625,0.5625
#> "Helene",0,0.5,0.5,0,0.25,0.5,0.125,0.5,0.125,0.125,0.25,0.125,0.125,0.125,0.125,0.5,1,0.3125,0.3125,0.3125
#> "Electre",0.0625,0.359375,0.265625,0.125,0.2734375,0.328125,0.32421875,0.375,0.32421875,0.44921875,0.2734375,0.32421875,0.32421875,0.38671875,0.57421875,0.5625,0.3125,1.0625,0.568359375,0.568359375
#> "Oreste",0.0625,0.359375,0.265625,0.125,0.2734375,0.328125,0.32421875,0.375,0.32421875,0.44921875,0.2734375,0.32421875,0.32421875,0.38671875,0.57421875,0.5625,0.3125,0.568359375,1.0625,0.568359375
#> "Hyphigenie",0.0625,0.359375,0.265625,0.125,0.2734375,0.328125,0.32421875,0.375,0.32421875,0.44921875,0.2734375,0.32421875,0.32421875,0.38671875,0.57421875,0.5625,0.3125,0.568359375,0.568359375,1.0625cat(paste(readLines("results/pedigreeRelationship.json", n=30), collapse = "\n"))
#> {
#> "relMat": [
#> {
#> "Pluto": 1,
#> "Zeus": 0,
#> "Leda": 0,
#> "Dione": 0,
#> "Tantale": 0.5,
#> "Europe": 0,
#> "Pelos": 0.25,
#> "Minos": 0,
#> "Pelopia": 0.25,
#> "Atree": 0.25,
#> "Catree": 0,
#> "Egiste": 0.25,
#> "Aerope": 0,
#> "Menelas": 0.125,
#> "Agamemnon": 0.125,
#> "Clytemnestre": 0,
#> "Helene": 0,
#> "Electre": 0.0625,
#> "Oreste": 0.0625,
#> "Hyphigenie": 0.0625,
#> "_row": "Pluto"
#> },
#> {
#> "Pluto": 0,
#> "Zeus": 1,
#> "Leda": 0,
#> "Dione": 0,The genotypic and phenotypic geno/testMarkerData01 and
pheno/testPhenoData01.csvdata used as example come from:
Keyan Zhao, Chih-Wei Tung, Georgia C. Eizenga, Mark H. Wright, M. Liakat Ali, Adam H. Price, Gareth J. Norton, M. Rafiqul Islam, Andy Reynolds, Jason Mezey, Anna M. McClung, Carlos D. Bustamante & Susan R. McCouch (2011). Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Comm 2:467 | DOI: 10.1038/ncomms1467, Published Online 13 Sep 2011.
The data geno/breedGame_geno.vcf.gz, pheno/breedGame_pheno.csv, and
breedGame_pedigree.csv are simulated data generated using
“PlantBreedGame”:
Flutre, T., Diot, J., and David, J. (2019). PlantBreedGame: A Serious Game that Puts Students in the Breeder’s Seat. Crop Science. DOI 10.2135/cropsci2019.03.0183le