create_genetic_map: Simulate Genetic Map
In arfesta/SimBreeder: Forward population breeding simulator

Description Usage Arguments Examples

View source: R/create_map.R

This function simulates the creation of a genetic map which mimics the genetic architecture of user defined inputs

create_genetic_map(num.chromos, map.length, num.markers, total.QTL, num.SNPQTL,
  distribute.loci = NULL, marker.distribution = NULL,
  map.dist = "haldane", chromosome.size.range = 0.2, total.loci = NULL,
  signif.digits = 2, marker.maf = NULL, seed = F, save = F)

`num.chromos`	The number of chromosomes to simulate
`map.length`	The genetic map length in centi-morgans
`num.markers`	Number of markers that can be used for genomic selection or estimated relatedness
`total.QTL`	The total number of QTL to place on the genetic map
`num.SNPQTL`	The number of total.QTL which will be SNPs
`map.dist`	Type of distance function to use in calculating recombination frequences. Options are: "haldane" & "kosambi". (Default = "haldane)
`chromosome.size.range`	The chromosome size range from the mean length of chromosomes (Default: 0.2)
`total.loci`	The total number of loci to be placed on genetic map
`signif.digits`	The number of significant digits to use (Default: 2)
`seed`	logical. Set seed so that genetic map is the same every time (Default: FALSE)
`save`	logical. Saves the output of genetic map (Default: FALSE)
`het.markers`	logical. Should all markers used be fully heterozygous? (Default: FALSE)

1	create_genetic_map(num.chromos = 12, map.length = 1800, num.markers = 120, total.loci = signif((120+2500)/12,digits = 2)*12, total.QTL = 2500, num.SNPQTL = 1960)