Get QTL genetic map

Retrieves the genetic map for the QTL of a given trait.

Usage

getQtlMap(trait = 1, sex = "A", simParam = NULL)

Arguments

trait

an integer for the

sex

determines which sex specific map is returned. Options are "A" for average map, "F" for female map, and "M" for male map. All options are equivalent if not using sex specific maps.

simParam

an object of SimParam

Value

Returns a data.frame with:

id

Unique identifier for the QTL

chr

Chromosome containing the QTL

site

Segregating site on the chromosome

pos

Genetic map position

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$nThreads = 1L
SP$addTraitA(5)

#Pull SNP map
getQtlMap(trait=1, simParam=SP)
#>        id chr site       pos
#> 1_4   1_4   1    4 0.3333333
#> 1_6   1_6   1    6 0.5555556
#> 1_7   1_7   1    7 0.6666667
#> 1_9   1_9   1    9 0.8888889
#> 1_10 1_10   1   10 1.0000000