getSnpMap {AlphaSimR}

Get SNP genetic map

Description

Retrieves the genetic map for a given SNP chip.

Usage

getSnpMap(snpChip = 1, sex = "A", simParam = NULL)

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$addSnpChip(5)

#Pull SNP map
getSnpMap(snpChip=1, simParam=SP)