rrollup: Applies rrollup function

In pmartR/pmartRqc: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Applies rrollup function

Description

This function applies the rrollup method to a pepData object for each unique protein and returns a proData object.

Usage

rrollup(pepData, combine_fn, parallel = TRUE)

Arguments

pepData	an omicsData object of class 'pepData'
combine_fn	logical indicating what combine_fn to use, defaults to median, other option is mean
parallel	logical indicating whether or not to use "doParallel" loop in applying rrollup function. Defaults to TRUE.

Details

In the rrollup method, peptides are scaled based on a reference peptide and protein abundance is set as the mean of these scaled peptides.

Value

an omicsData object of class 'proData'

References

Matzke, M. M., Brown, J. N., Gritsenko, M. A., Metz, T. O., Pounds, J. G., Rodland, K. D., ... Webb-Robertson, B.-J. (2013). A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics, 13(0), 493-503.

Polpitiya, A. D., Qian, W.-J., Jaitly, N., Petyuk, V. A., Adkins, J. N., Camp, D. G., ... Smith, R. D. (2008). DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics (Oxford, England), 24(13), 1556-1558.

pmartR/pmartRqc documentation built on April 25, 2024, 6:18 a.m.