make.contrast function

Builds the contrast matrix

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).

Returns

A constrat matrix

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)

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.