get_limma_results: Create limma DE analysis for all coefficients

In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

Create limma DE analysis for all coefficients

Description

This functions creates limma DE analysis

Usage

get_limma_results(
  normData,
  df_treatment_Ind,
  design.given,
  contrasts.matrix.given,
  coef.given.list,
  OUTPUT_Data_sample,
  comp_name,
  pCutoff.given = 0.05,
  FCcutoff.given = log2(1.2),
  forceResults = FALSE,
  EPIC = FALSE
)

Arguments

normData	dataframe to use as normalized values
df_treatment_Ind	Sample sheet with information for plotting
design.given	Matrix with design
contrasts.matrix.given	makeContrast object to test
coef.given.list	List of coefficients names to test.
OUTPUT_Data_sample	Output directory to save results
comp_name	Column name in sample sheet given to test.
pCutoff.given	Adjusted pvlaue cutoff. Default=0.05,
FCcutoff.given	Log Fold change cutoff. Default=log2(1.2),
forceResults	Set flag to force results if previously generated. Default=FALSE
EPIC	Boolean to indicate EPIC probes, avoid generating huge xlsx file. Default=FALSE

HCGB-IGTP/HCGB.IGTP.DAnalysis documentation built on April 13, 2025, 12:03 a.m.