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FDR-adjusting associations p-values grouped on BRITE hierachy

About

Project for Algorithmic Bioinformatics course taken by participants of Medbioinfo

This workflow will annotate associations provided with associated genes and KEGG Funtional hierachies. Using the distribution of for each feature group it calculates q-values and output visualisation (manhattan plots, p-value distribution etc).

Prerequisites

  • Python 3.7.3

    • Snakemake 5.7.4+
    • seaborn
    • pandas
    • matplotlib

  • R 3.5.2 +

    • biomaRt
    • tidyverse
    • magrittr
    • KEGGREST
    • reshape2

Setup

First clone this repo into desired location.

git clone https://github.com/JoelAAs/algobioing_project

For python packages I'd reccomend installing them through Conda.

The R to install run:

install.packages(c("tidyverse",  "magrittr", "reshape2", "BiocManager"))
BiocManager::install(c("biomaRt", "KEGGREST"))

Running

Move association files to input/ and add filename to python test = [] to the Snakefile.
Now just run snakemake like in your project folder. Observe that the header of the association file is assumed to be that of a plink .assoc file.

Output

A HTML repport can be found at results/{input_file}.html.