Description Usage Arguments Details Author(s) Examples
Create the matrix of all pairwise contrasts between parameters for the test.LC function
1 | makeAllContrasts(X, annot)
|
X |
the design matrix |
annot |
the annotation table of the individuals with the columns corresponding to the model variables |
This function create a contrasts matrix that can be used with the
test.LC
function. All pairwise comparisons for each
variable stratified into all other variables are returned.
Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | data(marty)
##Class label 0/1
marty.type.num <- ifelse(marty.type.cl=="Her2+",0,1)
#Annotation of the grade of tumor
grade <- factor(sample(c(1:3),23,rep=TRUE),labels=c("I","II","III"))
annot <- data.frame(type=marty.type.num, grade=grade)
rownames(annot) <- colnames(marty)
marty.lm <- lm(marty[1,]~ annot$grade * annot$type)
X <- model.matrix(marty.lm)
LC <- makeAllContrasts(X, annot)
|
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