getSnpMap: Get SNP genetic map
In AlphaSimR: Breeding Program Simulations

getSnpMap

R Documentation

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)

AlphaSimR documentation built on Nov. 2, 2023, 6:01 p.m.