iBAQ: iBAQ workflow

In arnesmits/DEPstoi: Stoichiometry analysis of label-free proteomics data

Description

iBAQ is a wrapper function running the entire analysis workflow for stoichiometry analysis using intensity-based absolute quantification (iBAQ)-based proteomics data.

Usage

iBAQ(results, peptides, contrast, bait, level = 1)

Arguments

results	List of SummarizedExperiment objects obtained from the LFQ wrapper function.
peptides	Data.frame, Peptide table from MaxQuant ('peptides.txt').
contrast	Character(1), The specific contrast for which to calculate stoichiometries.
bait	Character(1), The name of the protein to which all other proteins will be scaled for the relative stoichiometry.
level	Numerical(1), The level to which the bait will be scaled

Value

A data.frame with the relative stoichiometry data.

Examples

# load data and test for differentially enriched proteins
data <- GFPip
expdesign <- GFPip_ExpDesign
results <- LFQ(data, expdesign, 'MinProb', 'control', 'WT',
   filter = c('Reverse', 'Contaminant'), alpha = 0.05, lfc = 4.5)

# load peptide data and perform iBAQ-based stoichiometry analysis
peptides <- GFPip_pep
iBAQ(results, peptides, contrast = 'GFP_vs_WT', bait = 'Suz12')

arnesmits/DEPstoi documentation built on May 3, 2019, 4:31 p.m.