Builds the contrast matrix — make.contrast • mi4p

This function builds the contrast matrix

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

Thomas Burger, Quentin Giai-Gianetto, Samuel Wieczorek originally in the DAPAR package. Included in this package since DAPAR is to be removed from Bioconductor >= 3.15.

Examples

if (FALSE) {
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)
}