| rrollup {pmartR} | R Documentation |
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.