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/
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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)
- R script to extract:
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)