Compare gene clusters functional profile
Given a list of gene set, this function will compute profiles of each gene cluster.
compareCluster(geneClusters, fun = "enrichGO", data = "", ...)
geneClusters |
a list of entrez gene id. Alternatively, a formula of type Entrez~group |
fun |
One of "groupGO", "enrichGO", "enrichKEGG", "enrichDO" or "enrichPathway" . |
data |
if geneClusters is a formula, the data from which the clusters must be extracted. |
... |
Other arguments. |
A clusterProfResult instance.
Guangchuang Yu https://guangchuangyu.github.io
## Not run:
data(gcSample)
xx <- compareCluster(gcSample, fun="enrichKEGG",
organism="hsa", pvalueCutoff=0.05)
as.data.frame(xx)
# plot(xx, type="dot", caption="KEGG Enrichment Comparison")
## formula interface
mydf <- data.frame(Entrez=c('1', '100', '1000', '100101467',
'100127206', '100128071'),
group = c('A', 'A', 'A', 'B', 'B', 'B'),
othergroup = c('good', 'good', 'bad', 'bad', 'good', 'bad'))
xx.formula <- compareCluster(Entrez~group, data=mydf,
fun='groupGO', OrgDb='org.Hs.eg.db')
as.data.frame(xx.formula)
## formula interface with more than one grouping variable
xx.formula.twogroups <- compareCluster(Entrez~group+othergroup, data=mydf,
fun='groupGO', OrgDb='org.Hs.eg.db')
as.data.frame(xx.formula.twogroups)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.