make.contrast {mi4p}

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 originally in the DAPAR package. Included in this package since DAPAR was to be removed from Bioconductor >= 3.15.

Examples

## Not run: 
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)

## End(Not run)