Summarize DEGs Across Selected Assays

Summarizes the number of DEGs in each assay of a geneda object according to thresholds for adjusted p-value and log2 fold-change, separately reporting upregulated and downregulated genes.

SummarizeDEGs(object, alpha = 0.05, lfc1 = 1, lfc2 = 2, assays = NULL)

Arguments

object

A geneda object containing DEGs in its DEGs slot.

alpha

Numeric; adjusted p-value threshold. Default is 0.05.

lfc1

Numeric; lower log2 fold-change threshold. Default is 1.

lfc2

Numeric; higher log2 fold-change threshold. Default is 2.

assays

Optional character vector of assay names to summarize. Defaults to all assays in object@DEGs.

Value

A data.frame of DEG counts by assay and criteria.