Genomic data and code to accompany the SKAT analysis of Million Mutation Project strains dye-filling phenotypes reported in Timbers et al., bioRxiv, 2015. Specifically, this is the code used to generate Supplementary Tables 3-6.
- Bash Shell (version 3.2.57(1))
- Make (version 3.81)
- Perl (v5.18.2)
- Plink (v1.90b3.36)
- R (version 3.2.3)
- R packages:
- dplyr (version 0.4.3)
- fdrtool (version 1.2.15)
- plyr (version 1.8.3)
- pwr (version 1.1-3)
- SKAT (version 1.0.9)
- stringr (version 1.0.0)
This code assumes that you have put Plink
in your Bash Shell
's $PATH
. This can be
done by adding the following to .bash_profile
in your home directory (cd ~/
to get
there).
# added Plink
export PATH="/path/to/where/you/installed/plink:$PATH"
There is also a Docker image of the environment which the analysis was run in can be accessed here: https://hub.docker.com/r/ttimbers/mmp-dyf-skat/
- Clone this repository
- Navigate the Shell to the root directory of this project
- Type
make