Genomic data and code to accompany the SKAT analysis of Million Mutation Project strains dye-filling phenotypes reported in Timbers et al.
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README.md

Million-Mutation-Project-dye-filling-SKAT

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.

Dependencies

  • 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:
    1. dplyr (version 0.4.3)
    2. fdrtool (version 1.2.15)
    3. plyr (version 1.8.3)
    4. pwr (version 1.1-3)
    5. SKAT (version 1.0.9)
    6. 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/

How to use it

  1. Clone this repository
  2. Navigate the Shell to the root directory of this project
  3. Type make