de_deqms: Apply DEqMS to a protein-level ExpressionSet
In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

View source: R/stats_differential_abundance.R

de_deqms

R Documentation

Apply DEqMS to a protein-level ExpressionSet

Description

ref; PMID:32205417 ref; https://github.com/yafeng/DEqMS

Usage

de_deqms(eset, model_matrix, model_matrix_result_prop, doplot = FALSE)

Arguments

`eset`	protein-level log2 intensity matrix stored as a Biobase ExpressionSet. Note that it must contain protein metadata column 'npep' that holds integer peptide counts
`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"
`doplot`	create a QC plot?

Details

implementation follows example code from the vignette; https://bioconductor.org/packages/release/bioc/vignettes/DEqMS/inst/doc/DEqMS-package-vignette.html

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