In sarahodell/magicsim: What the Package Does (One Line, Title Case)

Simulating an F2 population with magic sim

The following uses magicsim to simulate 500 F2s from a cross between B73 and Mo17

  | B73 x Mo17|

      | F1 |

      | F2 |

A population of F1 lines are created, followed by 1 generation of selfing to make F2s

Installation

knitr::opts_chunk$set(echo = TRUE, warning=FALSE)
### Script to simulate 400 Double Haploid MAGIC lines

#devtools::install_github('sarahodell/magicsim',force = T)

library('magicsim')
library("data.table")
library("tidyverse")
library("ggplot2")

options(scipen=999)

The genetic map should have the following columns: 'chr': chromosome number (integer) 'pos': physical position of marker (integer) 'scaled_cM': genetic position of marker (scaled so that the first marker is 0) (float)

set.seed(1)
#read in your genetic map
gmap=fread('ogutmap_v4_ordered.csv',data.table=F)
#gmap=gmap[,c('chr','pos','scaled_cM')]
# The 2 initial founder maize lines. This could be anything
founders=c("Mo17","B73")

### Simulate chromosomes 1 throught 10
c=10
### Initialize the founders
B73=indv_init(chr=c,gmap,h1_donors=c("B73"),h2_donors=c("B73"))
Mo17=indv_init(chr=c,gmap,h1_donors=c("Mo17"),h2_donors=c("Mo17"))

Create the first round of F1s

We can create an F1 from the initial cross.

f1=make_f1(B73,Mo17,gmap,chroms=c)

Building an F2 Population.

Self 500 F1s once

n=500
gen=1

f2s=new("Pop",nIndv=n,indvlist=vector("list",length=n))
for(i in seq(1,n)){
  f2s@indvlist[[i]]=self(f1,c=c,ngen=gen,g_map=gmap)
}

Visualization

We can visualize chromsome 10 for 10 individuals in the population

pop_breaktable=make_pop_breaktable(f2s,c=10,het=T)
plot_Pop(pop_breaktable,n=10,c=10,het=T)

Can also do for all 10 chromosomes on one individual

indv_breaktable=make_indv_breaktable(f2s@indvlist[[1]])

plot_Indv(indv_breaktable)

If you want to construct a vcf file from the breakpoints, save the table to a file

fwrite(pop_breaktable,'F2_500_breaktable.txt',row.names=F,quote=F,sep='\t')

sarahodell/magicsim documentation built on Sept. 25, 2023, 8:12 a.m.