R code implementing QTL mapping of prepulse inhibition phenotypes in F1 crosses of common inbred mouse strains
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README.md

README.md

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."

License

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.

  • unc.F1.csv.gz Genotype data at 2,543,560 SNPs for F1 crosses of 29 inbred lab strains. These data were obtained from the UNC resource (link).

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.

Credits

The R code implementing the analysis procedures was developed by:
Laura Sittig, Kyle Engel and Peter Carbonetto
Department of Human Genetics
University of Chicago
June 2015