dea_algorithms: returns all DEA functions integrated with MS-DAP

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

returns all DEA functions integrated with MS-DAP

Description

available DEA functions

ebayes: wrapper for the eBayes function from the limma package (PMID:25605792) https://bioconductor.org/packages/release/bioc/html/limma.html. The eBayes function applies moderated t-statistics to each row of a given data matrix. It was originally developed for the analysis of RNA-sequencing data but can also be applied to a proteomics protein*sample data matrix. Doesn't work on peptide-level data because limma eBayes returns t-statistics per row in the input matrix, so using peptide-level data would yield statistics per peptide and translating those to protein-level statistics is not straight forward. Thus, with MS-DAP we first perform peptide-to-protein rollup (e.g. using MaxLFQ algorithm) and then apply the limma eBayes function to the protein-level data matrix.

This is in line with typical usage of moderated t-statistics in proteomics (e.g. analogous to Perseus, where a moderated t-test is applied to protein data matrix). This method will take provided covariates into account (if any). Implemented in function; de_ebayes

deqms: wrapper for the DEqMS package (PMID:32205417) https://github.com/yafeng/DEqMS, which is a proteomics-focussed extension of the limma eBayes approach that also weighs the number of peptides observed per protein to adjust protein statistics. MS-DAP will apply this function to the protein-level data matrix. This method will take provided covariates into account (if any). Implemented in function; de_deqms

msempire: wrapper for the msEmpiRe package (PMID:31235637) https://github.com/zimmerlab/MS-EmpiRe. This is a peptide-level DEA algorithm. Note that this method cannot deal with covariates! Implemented in function; de_msempire

msqrob: implementation of the MSqRob package, with minor tweak for (situationally) faster computation (PMID:26566788) https://github.com/statOmics/msqrob. This is a peptide-level DEA algorithm. This method will take provided covariates into account (if any). Implemented in function; de_msqrobsum_msqrob

msqrobsum: implementation of the MSqRob package (which also features MSqRobSum), with minor tweak for (situationally) faster computation (PMID:32321741) https://github.com/statOmics/msqrob. This is a hybrid peptide&protein-level DEA algorithm that takes peptide-level data as input; it first performs peptide-to-protein rollup, then applies statistics to this protein-level data matrix. This method will take provided covariates into account (if any). Implemented in function; de_msqrobsum_msqrob

Usage

dea_algorithms()

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