get_FDR_empirical: Add empirical p-values and adjusted p-values to a subset of...

In saeyslab/multinichenetr: MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Add empirical p-values and adjusted p-values to a subset of the DE output table.

Description

get_FDR_empirical Add empirical p-values and adjusted p-values to a subset of the DE output table. This is the function that works under the hood of 'add_empirical_pval_fdr'. Credits to Jeroen Gillis (cf satuRn package)

Usage

get_FDR_empirical(de_output_tidy, cluster_id_oi, contrast_oi, plot = FALSE)

Arguments

de_output_tidy	Data frame of DE results, containing at least the following columns: cluster_id, contrast, p_val, logFC.
cluster_id_oi	Indicate which celltype DE results should be filtered for.
contrast_oi	Indicate which contrast DE results should be filtered for.
plot	TRUE or FALSE (default): should we plot the z-score distribution?

Value

de_output_tidy dataframe (for the celltype and contrast of interest) with two columns added: p_emp and p_adj_emp.

saeyslab/multinichenetr documentation built on Jan. 15, 2025, 7:55 p.m.