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Schizophrenia_cross_disorder_scripts

The scripts herein detail the commands utilised for the analyses and figures described in Reay & Cairns 2019: Pairwise common variant meta-analyses of schizophrenia with other psychiatric disorders reveals shared and distinct gene and gene-set associations

The sample scripts are as follows:

  1. MAGMA_automation.py: Script for performing the MAGMA gene-based and set-based association, This script assumed MAGMA is either installed in the directory it is run from or accessible as PATH variable. Requires the following command line inputs:
    --gwasfile, GWAS summary statistics in the following format - SNP, CHR, BP, P
    --geneloc, Gene location file - ID, BP1, BP2
    --phenotype, GWAS phenotype name
    --bfile, Reference population plink binary fileset - .bed, .bim + .fam
    --samplesize, Sample size which GWAS performed on - cases + controls
    --genesets, Input pathways in standard MSigDB format, see MAGMA manual for further clarification
    Please refer to the MAGMA manual for more information

  2. FUSION_automation_sample_script.sh: These are the command line inputs used for the FUSION analyses in the manuscript

  3. Circular_manhattan.R: Commands used to construct the circular Manhattan plots in Figure 1

  4. Gene_set_forest_plot.R: Commands used to create the forest plots in Figure 2

  5. Manhattan_script.R: Sample commands used to create the Manhattan plots with a subset of genes highlighted (Figure 3)