R data package with Arabidopsis MAGIC lines genotypes for use with the R/qtl2 package.
You can install this package directly from GitHub (copy/paste this block of code to your console):
# install the remotes package if not installed already
if (!("remotes" %in% rownames(installed.packages()))){
install.packages("remotes")
}
# Install atMAGIC
remotes::install_github("tavareshugo/atMAGIC")
The package provides with a cross2
object with MAGIC line genotypes:
library(atMAGIC) # this loads qtl2 as well
# Load the data to the environment
data("kover2009")
# Look at its documentation for more details
?kover2009
This object only contains genotype data, with no phenotype information.
At the moment, R/qtl2 does not offer a function to add phenotypes to an
existing cross2
object. I’ve written a helper function to do this,
which is part of the qtl2helper
package (follow link for
installation instructions).
library(qtl2helper)
# Read example data
pheno <- read.table("http://mtweb.cs.ucl.ac.uk/mus/www/magic/MAGIC.phenotype.example.12102015.txt",
header = TRUE)
# Add to kover2009
kover2009 <- add_pheno(kover2009, pheno, idcol = "SUBJECT.NAME")
After this you can proceed with a similar analysis as explained in the R/qtl2 documentation for the diversity outbred mice. Very briefly:
# Calculate genotype probabilities
kover2009_probs <- calc_genoprob(kover2009)
# Run a QTL scan
kover2009_scan <- scan1(kover2009_probs, kover2009$pheno)
# Run permutations for genome-wide threshold (increase n_perm in real analysis)
kover2009_perm <- scan1perm(kover2009_probs, kover2009$pheno, n_perm = 10)
kover2009_threshold <- summary(kover2009_perm)
# Quick visualisation
plot(kover2009_scan, kover2009$pmap, lodcolumn = "days.to.bolt")
abline(h = kover2009_threshold[,"days.to.bolt"])
# Find peaks above certain threshold (should base it on permutation threshold from above)
find_peaks(kover2009_scan, kover2009$pmap, threshold = 10)
## lodindex lodcolumn chr pos lod
## 1 1 bolt.to.flower 4 48813 12.81461
## 2 1 bolt.to.flower 5 3177500 14.41196
## 3 2 days.to.bolt 1 19778899 12.54174
## 4 2 days.to.bolt 4 301329 30.22150
## 5 2 days.to.bolt 5 3176796 19.30336
## 6 3 days.to.germ 3 16163881 12.29746