QTL mapping of prepulse inhibition phenotypes in F1 panel derived from common inbred mouse strains
This repository contains code and data to accompany publication of the manuscript (in review), "Genome-wide association for prepulse inhibition in a panel of inbred F1 mice."
Copyright (c) 2015, Laura Sittig, Kyle Engel and Peter Carbonetto
The ppi-f1-gwas project repository is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See LICENSE for more details.
Overview of data files
Here is a brief summary of the files in the data directory:
pheno.csv Physiological and behavioural phenotype data collected on F1 mice that are crosses of inbred lab strains.
mda.F1.csv.gz Genotype data at 302,625 SNPs for F1 crosses of 29 inbred lab strains obtained from Mouse Diversity Genotyping Array web resource at Jackson Labs.
Overview of R source code files
Here is a brief summary of the key files in the code directory:
map.qtls.gemma.R R script for mapping QTLs in wild-type F1 mice using a linear mixed model (GEMMA) that corrects for possible confounding to due cryptic relatedness.
finemap.qtls.gemma.R R script for mapping QTLs using the higher resolution UNC SNP data.
functions.gemma.R Defines functions used to map QTLs separately on each chromosome using GEMMA.
The R code implementing the analysis procedures was developed by:
Laura Sittig, Kyle Engel and Peter Carbonetto
Department of Human Genetics
University of Chicago