de_ebayes: Apply limma::eBayes() function to a protein-level...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Apply limma::eBayes() function to a protein-level ExpressionSet

Description

ref; PMID:25605792 ref; https://bioconductor.org/packages/release/bioc/html/limma.html

Usage

de_ebayes(eset, model_matrix, model_matrix_result_prop)

Arguments

eset	protein-level log2 intensity matrix stored as a Biobase ExpressionSet
model_matrix	a stats::model.matrix() result that is supplied to limma::lmFit()
model_matrix_result_prop	the column name in model_matrix that should be returned as the resulting coefficient estimated by eBayes(). In MS-DAP workflows this is typically "condition"

Examples

## Not run: 
  # Minimal example:
  # Let `m` be a log2 protein intensity matrix matrix where
  # columns are samples and rows proteins.
  # Let `eset` be a Biobase::ExpressionSet that contains `m`.
  # Let `m_groups` be a character vector that describes the
  # sample group/condition for each column in `m`.
  # e.g. m_groups = c("WT", "WT", "WT", "KO", "KO", "KO")
  model_matrix = stats::model.matrix(~m_groups)
  de_ebayes(eset, model_matrix, colnames(model_matrix)[2])

## End(Not run)

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.