# load the phosphoproteomics dataset
data(HEK)
# load the kinase-substrate annoations
data(PhosphoSite)
# test enrichment on 8 directions in polar coordinate system.
bda <- directExplorer2d(Tc=HEK, annotation=PhosphoSite.mouse)
# the direction are denoted as follow for the two treatments vs control:
# ++: up-regulated in both treatments
# +*: up-regulated in the first treatment and unchanged in the second treatment
# +-: up-regulated in the first treatment and down-regulated in the second treatment
# *-: unchanged in the first treatment and down-regulated in the second treatment
# --: down-regulated in both treatments
# -*: down-regulated in the first treatment and unchanged in the second treatment
# -+: down-regulated in the first treatment and up-regulated in the second treatment
# *+: unchanged in the first treatment and up-regulated in the second treatment
# sort the most enriched phosphorylation sites and kinases on down-regulaiton from both
# treatments (i.e. "--") and displa the top-10 entries
bda$gene.tab[order(bda$gene.tab[,"--"]),][1:10,]
bda$path.tab[order(bda$path.tab[,"--"]),][1:10,]
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