make.contrast: Builds the contrast matrix

In samWieczorek/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Builds the contrast matrix

Description

This function builds the contrast matrix

Usage

make.contrast(design, condition, contrast = 1)

Arguments

design	The data.frame which correspond to the pData function of MSnbase
condition	xxxxx
contrast	An integer that Indicates if the test consists of the comparison of each biological condition versus each of the other ones (Contrast=1; for example H0:"C1=C2" vs H1:"C1!=C2", etc.) or each condition versus all others (Contrast=2; e.g. H0:"C1=(C2+C3)/2" vs H1:"C1!=(C2+C3)/2", etc. if there are three conditions).

Value

A constrat matrix

Author(s)

Thomas Burger, Quentin Giai-Gianetto, Samuel Wieczorek

Examples

utils::data(Exp1_R25_pept, package='DAPARdata')
design <- make.design(Biobase::pData(Exp1_R25_pept))
conds <- Biobase::pData(Exp1_R25_pept)$Condition
make.contrast(design, conds)

samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.