Two-Dimensional Group Benjamini-Hochberg (tdGBH) Procedure is a multiple testing procedure that offers enhanced power over traditional FDR control methods when the data presents two-way grouping structure. It reweights the p-values based on the informativeness of the respective grouping directions. It requires a matrix of p-values as input with rows and columns corresponding to the two grouping directions (e.g. genes by cell types). For details of the proposed method, please refer to the following paper:

Lu Yang, Pei Wang, Jun Chen. (2023) 2dGBH: Two-dimensional Group Benjamini-Hochberg Procedure for False Discovery Rate Control in Two-Way Multiple Testing of Genomic Data.

You can install tdGBH as follows:

# install.packages("devtools")
devtools::install_github("chloelulu/tdGBH")

The input matrix contains the raw p-values from testing the associations between the intake of 214 different nutrients and the abundance of 37 bacterial genera (Wu et al., 2021, Science). The output is the 2dGBH FDR-adjusted p-values (or q-values).

library(tdGBH)
data(P)
p.adj <- tdGBH(P)