zrollup: Applies zrollup function

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

Applies zrollup function

Description

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

Usage

zrollup(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 zrollup function. Defaults to TRUE.

Details

In the zrollup method, peptides are scaled as, pep_scaled = (pep - median)/sd, and protein abundance is set as the mean of these scaled peptides.

Value

an omicsData object of class 'proData'

References

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 March 4, 2024, 3:46 p.m.