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 1.33081889
#> Coll0002 -3.86384670
#> Coll0003 9.47277031
#> Coll0004 4.24236567
#> Coll0005 5.92835763
#> Coll0006 8.38889621
#> Coll0007 5.68567903
#> Coll0008 3.27343623
#> Coll0009 4.40608194
#> Coll0010 1.36342494
#> Coll0011 4.23352051
#> Coll0012 4.72179153
#> Coll0013 4.25707492
#> Coll0014 6.91564850
#> Coll0015 6.05117251
#> Coll0016 6.43686826
#> Coll0017 9.13095692
#> Coll0018 2.32898704
#> Coll0019 6.50661403
#> Coll0020 2.44771126
#> Coll0021 1.68588024
#> Coll0022 -0.05574874
#> Coll0023 1.17823306
#> Coll0024 1.58606344
#> Coll0025 5.21799241
#> Coll0026 -0.84148556
#> Coll0027 2.42903299
#> Coll0028 0.03955991
#> Coll0029 2.65465855
#> Coll0030 5.78191827
#> Coll0031 5.03515845
#> Coll0032 -1.43387116
#> Coll0033 1.16526582
#> Coll0034 1.57639763
#> Coll0035 2.13326123
#> Coll0036 4.75922869
#> Coll0037 1.90380791
#> Coll0038 3.49749326
#> Coll0039 -1.52048585
#> Coll0040 2.20230259
#> Coll0041 3.94585909
#> Coll0042 -2.80357182
#> Coll0043 -3.36204017
#> Coll0044 3.25325491
#> Coll0045 7.18228840
#> Coll0046 5.67914831
#> Coll0047 -1.28617182
#> Coll0048 0.39519550
#> Coll0049 10.01024152
#> Coll0050 1.20815849
#> Coll0051 11.74287977
#> Coll0052 7.80284217
#> Coll0053 6.07047948
#> Coll0054 1.54412467
#> Coll0055 -2.06851650
#> Coll0056 1.21124536
#> Coll0057 5.69113066
#> Coll0058 6.19018938
#> Coll0059 6.64560566
#> Coll0060 -0.47307625
#> Coll0061 -0.19835418
#> Coll0062 1.89770480
#> Coll0063 3.70419171
#> Coll0064 2.50227631
#> Coll0065 -2.09606355
#> Coll0066 8.33512437
#> Coll0067 1.24806400
#> Coll0068 2.37466865
#> Coll0069 3.74370686
#> Coll0070 9.97936128
#> Coll0071 6.61920358
#> Coll0072 4.25905818
#> Coll0073 1.25597810
#> Coll0074 7.86905252
#> Coll0075 5.94750022
#> Coll0076 -3.05304681
#> Coll0077 -3.19738377
#> Coll0078 -1.20636816
#> Coll0079 0.57028700
#> Coll0080 8.11025808
#> Coll0081 5.86601909
#> Coll0082 5.00307657
#> Coll0083 0.96023540
#> Coll0084 2.31676871
#> Coll0085 5.22509183
#> Coll0086 -2.51622551
#> Coll0087 4.07725382
#> Coll0088 1.03993167
#> Coll0089 3.62033933
#> Coll0090 2.61405095
#> Coll0091 1.76903421
#> Coll0092 4.63169784
#> Coll0093 -0.24560065
#> Coll0094 3.68384336
#> Coll0095 1.07232404
#> Coll0096 1.06381978
#> Coll0097 9.61093854
#> Coll0098 6.59338448
#> Coll0099 8.02812411
#> Coll0100 2.25227175