Convert a MArrayLM object with multiple contrasts into a list of DE results tables compatible with DeeDeeExperiment

This helper function extracts DE results for each contrast contained in a limma::MArrayLM object and reformats them into a list of standardized data frames suitable for integration in a DeeDeeExperiment object. Each resulting data frame includes renamed columns: logFC to log2FoldChange ,P.Value to pvalue, and adj.P.Val to padj

Usage

limma_list_for_dde(fit, number = nrow(fit), sort.by = "none")

Arguments

fit

A MArrayLM object, as produced by the limma workflow

number

An integer specifying the maximum number of genes to extract per contrast

sort.by

A character string specifying which statistic to rank the genes by. It must be one of the values accepted by the sort.by argument in the limma::topTable() function. Defaults to "none".

Value

A named list of DE results tables, one per contrast. Each table contains standardized columns and the list is annotated with metadata indicating its package origin (limma).

Details

The function assumes that each column in fit$coefficients corresponds to a contrast of interest. The names of the resulting list elements are taken directly from colnames(fit$coefficients). The names in the input object must therefore accurately reflect the intended contrast names.

See also

limma::topTable()

Examples

data("de_limma", package = "DeeDeeExperiment")
new_limma_list <- limma_list_for_dde(de_limma)
#> ℹ Returning 4 limma contrasts formatted for DeeDeeExperiment