Create population object from genotype data.frame

Usage

createPop(geno, SNPinfo, indNames = NULL, popName = NULL, verbose = TRUE)

Arguments

geno: [data.frame] genotype of the individuals encoded in allele dose. All individuals should be homozygotes. (value 0 or 2)
SNPinfo: [SNPinfo object] information about the individuals haplotypes' SNPs (see:SNPinfo)
indNames: NULL or character string vector specifying the individuals names. If NULL, rownames(geno) will be used.
popName: [character string] population's name.
verbose: [boolean] display information

Value

population object (see:population)

Examples

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)

print(exampleData$genotypes[1:5, 1:10])
#>          snp00006 snp00009 snp00011 snp00018 snp00026 snp00031 snp00035
#> Coll0001        2        2        2        0        2        2        2
#> Coll0002        0        2        2        2        0        0        0
#> Coll0003        2        2        2        0        2        2        2
#> Coll0004        0        2        2        2        0        0        0
#> Coll0005        2        2        2        0        2        2        2
#>          snp00036 snp00049 snp00052
#> Coll0001        0        0        0
#> Coll0002        2        2        2
#> Coll0003        0        0        0
#> Coll0004        2        2        2
#> Coll0005        0        0        0
example_pop <- createPop(geno = exampleData$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 !