Mmu2 QTL

This repository contains the raw data and the analysis scripts for mapping QTL on mouse chromosome 2 using CAST derived subcongenic strains. Checkout our paper :

Gularte-Mérida, et al. Overlapping mouse subcongenic strains successfully separate two linked body fat QTL on distal MMU 2 (2015) 16:16

Please not that all the files contained in the data/ directory are excluded from the BSD license. To use them for any purpose e.g. research or teaching, we would appreciate that you notify us by email.

Thank you in advance

data/

This directory contains mouse body fat mass data and its covariates used to perform a QTL mapping.
You may use the data for self learning and teaching purposes. However, we would appreciate that you
notify us at or
if you are distributing the data to a class or colleagues.

Plese don't hesitate to send us an email if you have any questions.

figures/

Contains an SVG file with the published figures.

analysis/

Contains shell scripts for deplyoing the analysis scripts in R.

System requirements : for the analysis you will require R:Language and Environment, and the packages r/qtl, boa, coda, hdrcde, and RColorBrewer. You can install these as : install.packages(c("qtl", "boa", "coda", "hdrcde", "RColorBrewer"))

All the scripts run on a single core, and most should work with ± 4GB of RAM. However, scripts for the repicated CIM analyses will require more RAM ± 16 GB or more.

R/qtl allows for mutlithreading with the n.cluster argument (requires packages snow and rlecuyer). In addition lapply and sapply loops can be run in paralell with snow using parLapply or parSapply. , For compatibility with most systems these options were not implemented.

src/

Scripts and other source code to perform the data analysis.

Our data repository does not contain the analysis scripts, and was the pre-publication repository.