trait object store information about a phenotypic trait
Public fields
name[string] Name of the trait
class"qualitative" or "quantitative" trait ("qualitative" not implemented yet)
qtn[character vector] names of the causal quantitative trait nucleotides (
length(qtn) == length(qtnEff)must betrue)qtnEff[numeric vector] quantitative trait nucleotides effects
Methods
Method new()
Create a new trait object.
Usage
trait$new(name = NULL, class = "quantitative", qtn = NULL, qtnEff = NULL)Arguments
name[character] name of the trait
class"quantitative" or "qualitative"
qtn[character vector] list of the quantitative trait nucleotides names implied in the trait
qtnEff[numeric vector] quantitative trait nucleotides effects (see details for more information).
Method gv()
Calculate the genetic values of a population
Arguments
pop[population class] population (see: population)
Examples
# create population
example_pop <- createPop(geno = exampleData$genotypes,
SNPinfo = SNPs,
popName = "Example population")
myTrait$gv(example_pop)Examples
## ------------------------------------------------
## Method `trait$new`
## ------------------------------------------------
mySpec <- specie$new(nChr = 10,
lchr = 10^6,
lchrCm = 100,
specName = "Geneticae Exempli")
#> A new species has emerged: Geneticae Exempli !
#>
SNPs <- SNPinfo$new(SNPcoord = exampleData$snpCoord,
specie = mySpec)
myTrait <- trait$new(name = "myTrait",
qtn = sample(SNPs$SNPcoord$SNPid, 100),
qtnEff = rnorm(100, sd = 0.5))
## ------------------------------------------------
## Method `trait$gv`
## ------------------------------------------------
# create population
example_pop <- createPop(geno = exampleData$genotypes,
SNPinfo = SNPs,
popName = "Example population")
#> Create population: Initialisation...
#> Create population: Create individuals...
#>
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#> Create population: Create population object...
#> Create population: Add individuals...
#>
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#> A new population created: Example population !
myTrait$gv(example_pop)
#> [,1]
#> Coll0001 3.8957318
#> Coll0002 -8.5590282
#> Coll0003 -9.3974029
#> Coll0004 -7.4569359
#> Coll0005 -14.3203086
#> Coll0006 -10.3572823
#> Coll0007 -5.2268542
#> Coll0008 -1.9545583
#> Coll0009 1.8377717
#> Coll0010 -1.0782440
#> Coll0011 -3.4290696
#> Coll0012 -4.3079093
#> Coll0013 -2.1225814
#> Coll0014 3.3516381
#> Coll0015 4.0142710
#> Coll0016 -2.5645038
#> Coll0017 -0.2593003
#> Coll0018 0.3297541
#> Coll0019 3.6508317
#> Coll0020 -4.7219192
#> Coll0021 2.1355660
#> Coll0022 -10.8940260
#> Coll0023 -9.3035674
#> Coll0024 -5.1860766
#> Coll0025 1.0025508
#> Coll0026 -8.6687643
#> Coll0027 2.3201724
#> Coll0028 -3.7192777
#> Coll0029 -3.1180431
#> Coll0030 -8.6771239
#> Coll0031 4.1883114
#> Coll0032 -1.5095017
#> Coll0033 -2.8879048
#> Coll0034 0.8603088
#> Coll0035 -3.0543282
#> Coll0036 4.0916538
#> Coll0037 -11.5851298
#> Coll0038 1.9960524
#> Coll0039 -5.8858337
#> Coll0040 -2.1907332
#> Coll0041 1.6180864
#> Coll0042 -5.7460986
#> Coll0043 -2.0878521
#> Coll0044 -5.3785177
#> Coll0045 -6.0830059
#> Coll0046 6.5716875
#> Coll0047 0.5303941
#> Coll0048 -2.1658336
#> Coll0049 -7.0924278
#> Coll0050 -3.1933443
#> Coll0051 9.6944820
#> Coll0052 0.4119142
#> Coll0053 -0.6371540
#> Coll0054 -2.1064161
#> Coll0055 -9.2618338
#> Coll0056 -2.8348676
#> Coll0057 4.4213618
#> Coll0058 2.0549973
#> Coll0059 -10.7454798
#> Coll0060 3.0709983
#> Coll0061 -1.0762653
#> Coll0062 -3.1198165
#> Coll0063 -2.9074041
#> Coll0064 -7.1592331
#> Coll0065 -8.2662867
#> Coll0066 -0.1856418
#> Coll0067 -8.2246253
#> Coll0068 3.4393838
#> Coll0069 -0.7228817
#> Coll0070 3.8837864
#> Coll0071 -3.2236122
#> Coll0072 -5.7184520
#> Coll0073 -6.1160669
#> Coll0074 -1.8374243
#> Coll0075 -2.2274717
#> Coll0076 -0.8120508
#> Coll0077 0.6758870
#> Coll0078 -3.3199234
#> Coll0079 -13.5251258
#> Coll0080 1.4912680
#> Coll0081 -6.3414462
#> Coll0082 3.3079534
#> Coll0083 -7.1247366
#> Coll0084 -4.1855997
#> Coll0085 -11.2423058
#> Coll0086 2.4032325
#> Coll0087 -7.2380905
#> Coll0088 -4.1220305
#> Coll0089 -5.8560442
#> Coll0090 -5.7129902
#> Coll0091 -8.7810970
#> Coll0092 6.3407421
#> Coll0093 -4.3729750
#> Coll0094 -6.6330472
#> Coll0095 -13.6628949
#> Coll0096 0.3565659
#> Coll0097 -11.3181132
#> Coll0098 -0.3659189
#> Coll0099 -2.6717402
#> Coll0100 2.9479336