Numerical data underlying graphs and summary statistics related to the ClassifyGxT method

This repository contains numerical data that underlies graphs and summary statistics for a manuscript originally posted as:Yuriko Harigaya, Nana Matoba, Brandon D. Le, Jordan M. Valone, Jason L. Stein, Michael I. Love*, William Valdar*. "Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes." doi: https://doi.org/10.1101/2024.08.03.605142 (* These authors contributed equally to this work.)

The data corresponds to the release v0.1.1 of the GitHub repository at https://github.com/yharigaya/classifygxt-paper. See main-figs.csv, supp-figs.csv, and tables.csv for the correspondence between the figures/tables and the numerical data files. The supp-figs.zip and supp-tables.zip contain the files for the supplementary figures and tables, respectively. The ClassifyGxT software is available from https://github.com/yharigaya/classifygxt.

Notes:

The individual genotype data that underlie Fig5A, Fig5C, Fig5E, Fig5G, Fig6A, Fig6C, Fig6E, S17 FigA, S17 FigC, S17 FigE, S17 FigG, S18 FigA, S18 FigC, and S18 FigE can be accessed via the Database of Genotypes and Phenotypes (dbGap) at https://www.ncbi.nlm.nih.gov/gap/ with the accession number phs003642.v1.p1 upon request and approval.

The partial ROC curves in S5 Fig and S12 Fig can be drawn using the data for the full ROC curves in S2 Fig and S11 Fig, respectively.

The numerical data underlying S7.2 Fig and S7.4 Fig are included in S7_Fig.csv and S7.3_Fig.csv, respectively.

In S3_Table_Data.csv and S4_Table_Data.csv, the "Index" column contains the indices for five randomly selected feature-SNP pairs.

In S5_Table_Data.csv and S6_Table_Data.csv, the "Marginal likelihood" column contains relative values of the sum of log-marginal likelihood across feature-SNP pairs.