data(gCMAPData)
## induce gene sets from a collection of z-scores
gene.set.collection <- induceCMAPCollection(
gCMAPData,
"z",
higher=2,
lower=-2)
sampleNames(gene.set.collection) <- c("set1", "set2", "set3")
## random score matrix
y <- matrix(rnorm(1000*6),1000,6,
dimnames=list(featureNames(gCMAPData), 1:6))
## set1 is differentially regulated
effect <- as.vector(members(gene.set.collection[,1]) * 2)
y[,4:6] <- y[,4:6] + effect
predictor <- c( rep("Control", 3), rep("Case", 3))
## run analysis and keep gene-level expression scores
res <- gsealm_score(
y,
gene.set.collection,
predictor=predictor,
nPerm=100,
keep.scores=TRUE)
res
## heatmap of expression scores for set1
set1.expr <- geneScores(res)[["set1"]]
heatmap(set1.expr, scale="none", Colv=NA, labCol=predictor,
RowSideColors=ifelse(
attr(set1.expr, "sign") == "up", "red", "blue"),
margin=c(7,5))
legend(0.35,0,legend=c("up", "down"),
fill=c("red", "blue"),
title="Annotated sign",
horiz=TRUE, xpd=TRUE)
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