This repository has all the code for analyses conducted for:

Lombardo, M. V., Eyler, L., Pramparo, T., Gazestani, V. H., Hagler, D. J., Chen, C.-H., Dale, A. M., Seidlitz, J., Bethlehem, R. A. I., Bertelsen, N., Carter Barnes, C., Lopez, L., Lewis, N. E., Pierce, K., & Courchesne, E. Atypical genomic cortical patterning in autism with poor early language outcome. bioRxiv. doi:10.1101/2020.08.18.253443.

All analysis is primarily conducted within R (R version 3.6.1 (2019-07-05) -- "Action of the Toes"), with the exception of the PLS analysis, which runs in MATLAB (R2019b).

PLS analysis uses the PLS toolbox in MATLAB that can be found here: https://www.rotman-baycrest.on.ca/index.php?section=84

Genetic cluster parcellations - GCLUST - can be found here: https://github.com/ENIGMA-git/GCLUST.

Plotting of the Chen GCLUST parcellation is implemented with ggseg: https://github.com/LCBC-UiO/ggsegChen.

acPCA can found here: https://github.com/linzx06/AC-PCA.

Gene lists for enrichment analyses can be found in the .Rdata files (e.g., enrichment_data2.Rdata, gandal_genelists.Rdata, etc).

The *.Rmd files explained below, show the code, and the accompanying html files show the code along with all the output generated by the code (e.g., statistical results, plots, etc).

_01_demographics.Rmd - Runs analysis on the clinical and demographic variables.

_01_covAdj* - Covariate adjustment of the gene expression and MRI data.

_02_WGCNA.Rmd - Runs the WGCNA analyses on gene expression data.

_03_batch_PLS*.m - Runs PLS analyses in MATLAB.

_03_plot* - Generates plots of PLS results.

_04_enrichmentAnalysis_sa_LV1_sexAdj_gentemp.Rmd - Enrichment analyses on SA LV1 results. _04_enrichmentAnalysis_ct_LV1_sexAdj_gentemp.Rmd - Enrichment analyses on CT LV1 results. _04_enrichmentAnalysis_ct_LV2_sexAdj_gentemp.Rmd - Enrichment analyses on CT LV2 results.

_05_FSanalysis_GenTemp.Rmd - Runs analyses on just the MRI data.

_06_psychENCODE.Rmd - Analysis of the psychENCODE data.