Builds the contrast matrix

Usage

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

Arguments

design: The data.frame which correspond to the colData() function of package MultiAssayExperiment.
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).
design.level: xxx

Value

A contrast matrix

Author

Thomas Burger, Quentin Giai-Gianetto, Samuel Wieczorek

Examples

data(subR25pept)
design <- make.design(SummarizedExperiment::colData(subR25pept))
conds <- design.qf(subR25pept)$Condition
make.contrast(design, conds)
#> [1] "( ConditionA )/ 1 -( ConditionB )/ 1"