Extract the DE results from eBayes fit of perform_limma function.

Extract the DE results from eBayes fit of perform_limma function.

Usage

extract_limma_DE(
  fit,
  comparisons,
  logFC = TRUE,
  logFC_up = 1,
  logFC_down = -1,
  p_adj = TRUE,
  alpha = 0.05
)

Arguments

fit

eBayes object resulting from perform_limma method

comparisons

Vector of comparisons that are performed in the DE analysis (from specify_comparisons method)

logFC

Boolean specifying whether to apply a logFC threshold (TRUE) or not (FALSE)

logFC_up

Upper log2 fold change threshold (dividing into up regulated)

logFC_down

Lower log2 fold change threshold (dividing into down regulated)

p_adj

Boolean specifying whether to apply a threshold on adjusted p-values (TRUE) or on raw p-values (FALSE)

alpha

Threshold for adjusted p-values or p-values

Value

Data table with limma DE results