de_msqrobsum_msqrob: Wrapper function for msqrob, using the implementation from...
In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

View source: R/stats_differential_abundance.R

de_msqrobsum_msqrob

R Documentation

Wrapper function for msqrob, using the implementation from the msqrobsum package

Description

note that this is the final version of this algorithm provided by its authors, and is no longer maintained; https://github.com/statOmics/msqrob only difference with the GitHub version is that code included here has minor adaptions to situationally improve multithreading (i.e. speeds up computation a bit, on some systems)

Usage

de_msqrobsum_msqrob(
  eset,
  model_matrix,
  model_matrix_result_prop,
  use_peptide_model,
  random_variables = NULL
)

Arguments

`eset`	a Biobase ExpressionSet that contains the peptide log2 intensities
`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"
`use_peptide_model`	if `TRUE`, apply msqrob. if `FALSE`, apply msqrobsum
`random_variables`	optionally, an array of column names in the sample metadata table that should be used as additional regression variables