qrollup: Applies qrollup function

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

Applies qrollup function

Description

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

Usage

qrollup(pepData, qrollup_thresh, combine_fn, parallel = TRUE)

Arguments

pepData	an omicsData object of class 'pepData'
qrollup_thresh	numeric value between 0 and 1 inclusive. Peptides above this threshold are used to roll up to the protein level
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 qrollup function. Defaults to TRUE.

Details

In the qrollup method, peptides are selected according to a user selected abundance cutoff value (qrollup_thresh), and protein abundance is set as the mean of these selected 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 documentation built on Oct. 15, 2024, 1:06 a.m.