Retrieves the genetic map for a given SNP chip.
Arguments
- snpChip
an integer. Indicates which SNP chip's map to retrieve.
- 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 SNP
- chr
Chromosome containing the SNP
- 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$addSnpChip(5)
#Pull SNP map
getSnpMap(snpChip=1, simParam=SP)
#> id chr site pos
#> 1_2 1_2 1 2 0.1111111
#> 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_10 1_10 1 10 1.0000000