normalizeData: Normalize proteus data

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Normalize proteus data

Description

normalizeData normalizes the intensity table in a proteusData object, using the provided normalizing function.

Usage

normalizeData(pdat, norm.fun = normalizeMedian)

Arguments

pdat	A proteusData object with peptide or protein intensities.
norm.fun	A normalizing function.

Details

The normalizing function, specified by norm.fun needs to normalize columns of a numerical matrix. The input is a matrix and the output is a normalized matrix. The default value points to normalizeMedian, Proteus's function normalizing each column to its median. Other functions can be used, for example normalizeQuantiles from the limma package.

Value

A proteusData object with normalized intensities.

Examples

library(proteusLabelFree)
data(proteusLabelFree)
prodat.med <- normalizeData(prodat, norm.fun=normalizeMedian)

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.