subset_protein_eset_for_dea: helper function to double-check we don't submit an...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

helper function to double-check we don't submit an ExpressionSet with too few values to DEA

Description

helper function to double-check we don't submit an ExpressionSet with too few values to DEA

Usage

subset_protein_eset_for_dea(
  eset,
  model_matrix_result_prop,
  is_peptide,
  method_name,
  min_values = NULL
)

Arguments

eset	a Biobase ExpressionSet
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"
is_peptide	boolean indicating peptide-level (FALSE = protein-level)
method_name	label for printing error messages
min_values	minimum number of data points in each condition. Alternatively, use options(msdap.dea.minvalue = 5)

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