Run DESeq2 differential analysis. — run_deseq • clover

Wrapper around DESeq2::DESeqDataSetFromMatrix() and DESeq2::DESeq() for tRNA abundance or charging data.

Usage

run_deseq(count_matrix, coldata, design, ...)

Arguments

count_matrix: An integer count matrix (from abundance_count_matrix() or charging_count_matrix()).
coldata: A data frame of sample metadata (from build_coldata()).
design: A formula specifying the design (e.g., ~ condition or ~ condition + charge_status + condition:charge_status).
...: Additional arguments passed to DESeq2::DESeq().

Value

A DESeqDataSet object.

Examples

if (FALSE) { # \dontrun{
dds <- run_deseq(mat, coldata, design = ~ condition)
} # }