This repository contains code used in the AAB and QTAB stool metagenomics analysis, and accompanying the paper titled, "Autism-gut microbiome connections may reflect autism-related dietary diversity".

metagenomics_analysis_taxonomic_manuscript.Rmd

• contains code for most analyses (eg. microbiome diversity, differential abundance, linear models)
• N.B. the code contained here is specific to the taxonomic for demonstration purposes. However, where mentioned in the manuscript, identical analyses were performed for functional datasets.

diet/

• AES_PCs_ACRC_QTAB_manuscript.html
  • .html knitted .Rmd document
  • includes code and figures from exploratory analysis of dietary data

osca_variancecomponent/

• metagenomics_analysis_osca_prep_manuscript.Rmd

  • .Rmd file used to pre-process microbiome count data (taxonomic and functional).
  • output of this code is used as input into OSCA, using commands in metagenomics_analysis_osca_manuscript.sh

• metagenomics_analysis_osca_manuscript.sh

  • .sh file with OSCA commands to generate ORMs, and to perform variance component analysis

linktaxafunc/

• metagenomics_analysis_linktaxafunc_manuscript.R
  • R script to extract:
    • count table for genes directly and specifically mapping to Romboutsia timonensis ("direct" analysis)
    • count table for genes that are within the Romboutsia timonensis genome, but can be encoded by any other species ("indirect" analysis)
• metagenomics_analysis_linktaxafunc_ancom_direct_manuscript.R
  • R code used to perform the "direct" analysis
  • input the "direct" analysis output from metagenomics_analysis_linktaxafunc_manuscript.R (eg. "aab_Romboutsia.timonensis_MICROBAgenes.txt")
  • differential abundance analysis (ANCOMv2.1)