magicdesign
Introduction
Welcome to 
magicdesign !
MAGIC (Multiparental Advanced Generation Inter-Cross) is a highly recombined population of multiple founders. MAGIC population is a versatile genetic resource for quantitative trait locus (QTL) mapping, fine-mapping, GxE dissection, genomic prediction, breeding and many more. Please check this out for an in-depth review of MAGIC.
magicdesign is an R package devoted to creating and testing MAGIC population designs via simulations. Click here for detailed instructions on installation and usage. Due to a recent change in github username, the vignette has not been updated to reflect the change. Please use the new installation link instead:
old: devtools::install_github("cjyang-sruc/magicdesign")
new: devtools::install_github("cjyang-work/magicdesign")
Frequently asked questions (FAQs)
1. How to use magicdesign?
First, make sure you have devtools installed in R. Skip this if you already have devtools.
install.packages("devtools")
Next, install magicdesign.
devtools::install_github("cjyang-work/magicdesign")
If the installation is successful, run the following:
library(magicdesign)
Detailed user instructions can be found here.
2. Which functions in magicdesign do I need?
-
magic.eval: create a MAGIC population design and simulate the population. -
magic.summary: tabulate the information of all designs. -
magic.plot: plot the distributions of recombinant haplotypes and founder genomes from all designs. -
magic.ped2plot: plot the pedigree of a MAGIC population design.
4. How do I create a MAGIC population with full design?
mpop <- magic.eval(m=8, m=45, reps=c(1,1,2), self=c(0,0,4), balanced=T)
5. How do I create a MAGIC population with partial balanced design?
mpop <- magic.eval(m=8, m=1, reps=c(1,1,10), self=c(0,0,4), balanced=T)
6. How do I create a MAGIC population with partial unbalanced design?
mpop <- magic.eval(m=8, m=7, reps=c(1,1,10), self=c(0,0,4), balanced=F)
7. How do I create a MAGIC population with basic design?
mpop <- magic.eval(m=8, m=0, reps=c(1,4,20), self=c(0,0,4))
8. How do I create a MAGIC population with custom design?
cped <- cbind(1:106, c(rep(0,4), 1, 3, rep(5,100)), c(rep(0,4), 2, 4, rep(6,100)), c(rep(0,4), rep(1,2), rep(2,100)))
mpop <- magic.eval(ped=cped)
9. Which R version do I need?
magicdesign is built in R version 4.0.3 and it should work with any newer version of R. I have not tested magicdesign in older versions so it may or may not work in older R versions.
10. Which are the supported platforms?
magicdesign is built in Windows, but it should work in Mac or Linux.
11. What are the computer requirements?
Nothing specific, but a fast processor (>2 GHz) with decent amount of RAM (>4 Gb) would be nice. magicdesign itself does not require more than one processor core, but I am not sure if its dependency AlphaSimR uses multiple cores.
Contact us
You can reach me at cyang@sruc.ac.uk for any question or suggestion.
Reference
Yang CJ, Edmondson RN, Piepho H-P, Powell W & Mackay I (2021) Crafting for a better MAGIC: systematic design and test for multiparental advanced generation inter-cross population. G3 11: jkab295. [Link]