Applies rrollup function

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

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.

Value

an omicsData object of class 'proData'

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.

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.