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Run differential expression analysis with edgeR/limma-voom

run_deg_analysis.Rd

Filters low-expression genes, applies TMM normalization, runs voom transformation, fits a linear model, and returns the top differentially expressed genes via limma::topTable.

Usage

run_deg_analysis(counts, coldata, group_col, ref_level = NULL)

Arguments

counts

A raw count matrix (genes x samples).

coldata

A data frame of sample metadata whose row names match the column names of counts.

group_col

Character. Name of the column in coldata used as the grouping factor for differential expression.

ref_level

Character or NULL. Reference level for the group factor. If NULL, the default factor ordering is used.

Value

A data frame of differentially expressed genes (p.adj < 0.05) as returned by limma::topTable, with columns logFC, AveExpr, t, P.Value, adj.P.Val, and B.