iTRAQ2GroupAnalysis {protViz}

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)