adjust_DE_cutoffs {DEET}

adjust_DE_cutoffs

Description

Utility function to adjust mean expression, FDR, and log2FC cutoffs of the database of DEGs inputted into DEET.

Usage

adjust_DE_cutoffs(
  DEET_combined,
  redo_pathways_instructions = FALSE,
  baseMean = 1,
  abslog2FoldChange = 0,
  padj = 0.05
)

Arguments

DEET_combined

The databank of the differential expression enrichment tool. Appropriate inputs here are "DEET_example_data" stored within DEET, the "DEET_combined.rda" file from the DEET stable repositoy found at X, and the DEET database developmental repository found at Y. The DEET_dataset is a named list where details of it's structure can be found ?DEET_example_data.

redo_pathways_instructions

Boolean value specifying whether to print the instructions required to update all pathway enrichments based on new DE cutoffs.

baseMean

Change the mean-expression cutoff.

abslog2FoldChange

Change the log2 Fold-change cutoff.

padj

Change the FDR-adjusted p-value cutoff.

Value

The DEET_combined object but with the user-inputted expression, log2FC, and FDR-adjusted p-value cutoffs. DEET_gmt_DE is also updated to the new cutoffs.

Author(s)

Dustin Sokolowski

Examples

data("DEET_example_data")
DEET_cutoff <- adjust_DE_cutoffs(DEET_example_data, abslog2FoldChange = 1, padj = 0.01)