dlPFCSchizophreniaRNA

Code for replicating analyses of:

"DLPFC Transcriptome Defines Two Molecular Subtypes of Schizophrenia"

Elijah F W Bowen
Jack L Burgess
Richard Granger
Joel E Kleinman
C Harker Rhodes

Installation

Once the below requirements are installed, the code will run without any build/compilation steps. You may check out this repository or simply download a zip. Please watch for new commits.

Requirements

• R (validated to run on versions 3.3.2 linux and 3.4.3 windows)
• RStudio (highly recommended since code are .Rmd markdown files, not .R scripts)
• R CRAN packages:
  • robust
  • robustlmm
  • WGCNA
  • igraph
  • statmod
  • stringr
• Certain scripts also require BioConductor packages, which are best installed from the BioConductor folks:
  • beadarray
  • edgeR
  • GenomicFeatures
  • lumi
  • illuminaHumanv4.db

Data

This code runs on data which is access-controlled by third parties (dbGaP study accession phs000979.v1.p1, CommonMind Consortium http://www.synapse.org/cmc). We cannot redistribute the data, but feel free to email us with questions.

Description of code

Scripts are numbered in a reasonable sequential order.

• NIH dataset
  • Pre-processing
    • 1-Format_phenotype_data.Rmd
    • 2-Format_idat_files.Rmd
    • 3-Filter_dlpfc_array_data.Rmd
  • Analyses
    • 4-Sz_cohort_demographics.Rmd
    • 5-Robust_lmer.Rmd
    • 6a-Cluster_schizophrenics.Rmd
    • 6b-Perturbation_stability_of_clustering.Rmd
    • 6c-Antipsychotics.Rmd
    • 6c-Subgroup_demographics.Rmd
    • 6d-Graphical_analysis.Rmd
    • 7a-Robust_lmer_with_sz_subtype_1.Rmd
    • 7b-Robust_lmer_with_sz_subtype_2.Rmd
    • 7-Figures_and_tables.Rmd
    • 7-Figures_and_table_from_residuals.Rmd
• CMC dataset
  • Pre-processing
    • 8a-Preprocess_cmc_data.Rmd
  • Analyses
    • 8b-CMC_cohort_demographics.Rmd
    • 8c-Pitt_cohort_de_analysis.Rmd
    • 8d-Clustering_of_pitt_cohort_schizophrenics