iTRAQ2GroupAnalysis: iTRAQ two group analysis

In protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

iTRAQ two group analysis

Description

The function performes a two group analysis with a t-test for data sets like iTRAQ. Result files are generated where the 2 groups are compared for each protein, while a p-value is calculated. If plot equals TRUE, the boxplots are drawn.

Usage

    iTRAQ2GroupAnalysis(data, group1, group2, 
        INDEX, FUN=function(x){return(x)}, plot)

Arguments

data	a data set like iTRAQ.
group1	a vector of column ids.
group2	a vector of column ids.
INDEX	list of factors, each of same length as X. The elements are coerced to factors by as.factor.
FUN	function for doing the data transformation, e.g. log, asinh.
plot	boolean. if TRUE boxplots are drawn.

Details

t.b.d.

Author(s)

Christian Panse, Jonas Grossmann 2011

Examples

       data(iTRAQ)
       par(mfrow=c(2,3))
       qProt<-iTRAQ2GroupAnalysis(data=iTRAQ, 
        group1=c(3,4,5,6), 
        group2=7:10, INDEX=iTRAQ$prot, plot=TRUE)
       qProt
       qPeptide<-iTRAQ2GroupAnalysis(data=iTRAQ, 
        group1=c(3,4,5,6), 
        group2=7:10, 
        INDEX=paste(iTRAQ$prot,iTRAQ$peptide), plot=FALSE)

protViz documentation built on May 29, 2024, 8:21 a.m.