top_markers_dds: Top markers per group from pseudobulk DESeq2 results

In presto: Fast Functions for Differential Expression Using Wilcoxon and AUC

Top markers per group from pseudobulk DESeq2 results

Description

Filters and ranks the long-form output of pseudobulk_deseq2() to give the most distinguishing features per group. The filtering arguments combine multiplicatively, then the top n features per group are kept by descending Wald statistic and pivoted into wide form. Counterpart to top_markers() for Wilcoxon-based results.

Usage

top_markers_dds(res, n = 10, pval_max = 1, padj_max = 1, lfc_min = 1)

Arguments

res	Long-form DESeq2 results from pseudobulk_deseq2(). Must have columns group, feature, pvalue, padj, log2FoldChange, and stat.
n	Number of top features to return per group. Default 10.
pval_max	Filter features with raw pvalue > pval_max. Default 1 (no filter).
padj_max	Filter features with adjusted padj > padj_max. Default 1 (no filter).
lfc_min	Filter features with log2FoldChange < lfc_min. Default 1 keeps only upregulated features; set to 0 to include downregulated as well, or -Inf to disable.

Value

tibble in wide form: a rank column (1..n) and one column per group containing the gene identifier of the top-ranked feature at that rank. Cells are NA for groups that have fewer than n features passing the filters.

See Also

pseudobulk_deseq2(), top_markers()

presto documentation built on Sept. 30, 2026, 5:13 p.m.