The GitHub repository includes several folders with different functionalities:
"apoe2_paper_stats_volume":
Contains R files that compute and visualize descriptive statistics based on brain region volume data. Requires extracting data from the "individual_label_statistics.zip" file.
"mice_with_symbol":
Includes an R file and an input file to add symbols to RNA normalized count.
"multi_cca_git":
Contains the "r_reader_connectome.R" file, which reads individual connectome, RNA, and phenotype data. Generates three output files: "connectivity.rda", "RNA_data.rda", and "response.rda". These files serve as input for SMCCA (Sparse Multiple Canonical Correlation Analysis).
"apoe2_rna_sig_age", "apoe2_rna_sig_sex", and "winding_multi_cca":
Include the SMCCA files "multicca.R". Each folder has its own purpose and data specifications. "winding_multi_cca" folder also includes additional behavioral data, such as winding number.
"winding_multi_cca":
Contains "d1_5_anovas.R" and "winding_repeated_day1-5.R" files. Responsible for descriptive statistics on different behavioral probe data.
"brainconnsetting.R" and "bootcca_multi_cca.R":
Visualize 3D brain results. Compute the 95% bootstrap confidence interval after running "multicca.R".
"multi_cca_volcano":
Includes two folders, "apoe2_rna_sig_age" and "apoe2_rna_sig_sex". These folders contain R files to plot volcano plots after SMCCA filtering. The input for these files is derived from the results of "apoe2_rna_sig_sex" and "apoe2_rna_sig_age", specifically the "RNA_result_ordered.xlsx" file.