regressIntensity: Regression based analysis

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

Regression based analysis

Description

Performs linear regression on protein intensities based on selected protein (qPLEX-RIME bait)

Usage

regressIntensity(MSnSetObj, ProteinId, controlInd = NULL, plot = TRUE)

Arguments

MSnSetObj	MSnSet; an object of class MSnSet
ProteinId	character; Uniprot protein ID
controlInd	numeric; index of IgG within MSnSet
plot	character; Whether or not to plot the QC histograms

Details

This function performs regression based analysis upon protein intensities based on a selected protein. In qPLEX RIME this method could be used to regress out the effect of target protein on other interactors. This function corrects this dependency of many proteins on the target protein levels by linear regression. It sets the target protein levels as the independent variable (x) and each of the other proteins as the dependent variable (y). The resulting residuals of the linear regressions y=ax+b are the protein levels corrected for target protein dependency.

Value

An object of class MSnSet (see MSnSet-class). This consists of corrected protein levels. In addition, the function can also plot histograms of correlation of target protein with all other proteins before and after this correction.

Examples

data(human_anno)
data(exp3_OHT_ESR1)
MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, 
                               metadata=exp3_OHT_ESR1$metadata_qPLEX1,
                               indExpData=c(7:16), 
                               Sequences=2, 
                               Accessions=6)
MSnset_P <- summarizeIntensities(MSnSet_data, sum, human_anno)
IgG_ind <- which(pData(MSnset_P)$SampleGroup == "IgG")
MSnset_reg <- regressIntensity(MSnset_P, 
                               controlInd=IgG_ind, 
                               ProteinId="P03372")

crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.