compareCluster: Compare gene clusters functional profile

In GuangchuangYu/clusterProfiler: A universal enrichment tool for interpreting omics data

Compare gene clusters functional profile

Description

Given a list of gene set, this function will compute profiles of each gene cluster.

Usage

compareCluster(
  geneClusters,
  fun = "enrichGO",
  data = "",
  source_from = NULL,
  ...
)

Arguments

geneClusters	a list of entrez gene id. Alternatively, a formula of type Entrez~group or a formula of type Entrez | logFC ~ group for "gseGO", "gseKEGG" and "GSEA".
fun	One of "groupGO", "enrichGO", "enrichKEGG", "enrichDO" or "enrichPathway" . Users can also supply their own function.
data	if geneClusters is a formula, the data from which the clusters must be extracted.
source_from	If using a custom function in "fun", provide the source package as a string here. Otherwise, the function will be obtained from the global environment.
...	Other arguments.

Value

A clusterProfResult instance.

Author(s)

Guangchuang Yu https://yulab-smu.top

See Also

compareClusterResult-class, groupGO enrichGO

Examples

## 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")
dotplot(xx)

## formula interface
mydf <- data.frame(Entrez=c('1', '100', '1000', '100101467',
                            '100127206', '100128071'),
                   logFC = c(1.1, -0.5, 5, 2.5, -3, 3),
                   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)

GuangchuangYu/clusterProfiler documentation built on Nov. 30, 2024, 3:25 a.m.