README.md

Cerebellum

This repository contains the code used for the analyses described in our manuscript "Traut et al. (2017). Cerebellar Volume in Autism: Literature Meta-analysis and Analysis of the Autism Brain Imaging Data Exchange Cohort. Biological Psychiatry. https://doi.org/10.1016/j.biopsych.2017.09.029" (Preprint: https://www.biorxiv.org/content/10.1101/104984v3).

Analysis of cerebellar volumes and areas differences between individuals with ASD and controls

Meta-analysis of the literature

To compute the meta-analysis and generate the figures, source the file meta-analysis.R in a R session.
The studies have to be listed in the file means-[roi].txt containing the required fields with the variable suffix set to [roi].

Analysis of Abide

Linear models were fit to evaluate the effect of group and covariables on cerebellum volume using the ABIDE 1 dataset (http://fcon_1000.projects.nitrc.org/indi/abide/). The script analyse-abide.R can be used to run them.

Meta-analysis of Abide

The script prepare-meta-abide.R can be run to prepare Abide data for meta-analysis. It splits data by site and remove individuals to ensure age and sex matching between groups. Mean and standard deviations of volumes for each group by site are then computed and writen to the file means-abide-Cbl.txt. Meta-analysis can then be computed with meta-analysis.R by setting suffix to abide-Cbl.

Other scripts

• meta-combin.R: performs a meta-analysis with the literature and abide combined
• meta-exec.R: performs a meta-analysis (similar to meta-analysis.R but no plot is produced).
• p-curve.R: draws p-curves from test statistics. Code was adapted from the source of the p-curve app: http://p-curve.com/app4/app 4.05.r by Uri Simonsohn, Leif D. Nelson and Joseph P. Simmons.
• result-tables-abide.R: generates report tables for the meta-analysis of the literature.
• result-tables-mod.R: generates report tables for the meta-analysis of Abide.