limma_DE_function: Create limma DE analysis
In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

limma_DE_function

R Documentation

Create limma DE analysis

Description

This functions creates limma DE analysis

Usage

limma_DE_function(
  efit_3,
  normData,
  df_treatment_Ind,
  design.given,
  contrasts.matrix.given,
  coef.given,
  OUTPUT_Data_sample,
  comp_name,
  numerator,
  denominator,
  pCutoff.given = 0.05,
  FCcutoff.given = log2(1.2),
  forceResults = FALSE,
  EPIC = FALSE
)

Arguments

`efit_3`	Ebayes fit results
`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`	One coefficient to test.
`OUTPUT_Data_sample`	Output directory to save results
`comp_name`	Column name in sample sheet given to test.
`numerator`	Comparison numerator.
`denominator`	Comparison denominator.
`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