get_stoichiometry: Relative stoichiometry

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

Description

get_stoichiometry calculates the relative stoichiometries of all differentially enriched proteins.

Usage

get_stoichiometry(dep, ibaq, contrast, bait, level = 1)

Arguments

dep	SummarizedExperiment, Proteomics dataset in which differential enriched proteins are annotated by add_rejections.
ibaq	Data.frame, iBAQ table generated by merge_ibaq.
contrast	Character(1), The specific contrast for which to calculate the stoichiometries.
bait	Character(1), The name of the protein to which all other proteins will be scaled.
level	Numerical(1), The level to which the bait will be scaled.

Value

A data.frame with relative stoichiometry values.

Examples

# load data
proteins <- GFPip
proteins <- data_unique <- make_unique(proteins, 'Gene.names', 'Protein.IDs')
exp_design <- GFPip_ExpDesign
peptides <- GFPip_pep

# Test for differential enriched proteins
se <- import_MaxQuant(proteins, exp_design,
    filter = c("Reverse", "Contaminant"))
processed <- process(se, fun = "MinProb")
dep <- analyze_dep(processed, 'control', 'WT', lfc = 4.5)

# Merge iBAQ intensities of proteins that have shared peptides
ibaq <- merge_ibaq(data_unique, peptides)

# Calculate relative stoichiometry versus 'Suz12' in the 'GFP_vs_WT' contrast
stoi <- get_stoichiometry(dep, ibaq, contrast = 'GFP_vs_WT', bait = 'Suz12')

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