2-Group Comparison of enrichment results and further clustering and visualizing
compareGT.Rd
See `?EnrichGT()`
Usage
compareGT(
obj.test,
obj.ctrl,
name.test = NULL,
name.ctrl = NULL,
ClusterNum = 15,
P.adj = 0.05,
force = F,
nTop = 10,
method = "ward.D2",
...
)
Arguments
- obj.test
the enriched object from tested group. WARNING: `obj.test` and `obj.ctrl` should come from same database (e.g. GO Biological Process(GOBP)).
- obj.ctrl
the enriched object from control group. WARNING: `obj.test` and `obj.ctrl` should come from same database (e.g. GO Biological Process(GOBP)).
- name.test
optional, the name of the testing group. If is `NULL`, the object name of `obj.test` will be used.
- name.ctrl
optional, the name of the control group. If is `NULL`, the object name of `obj.ctrl` will be used.
- ClusterNum
how many cluster will be clustered
- P.adj
p.adjust cut-off. To avoid slow visualization, you can make stricter p-cut off.
- force
ignore all auto-self-checks, which is useful
- nTop
keep n top items according to p-adj in each cluster.
- method
the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
- ...
Others options.
Value
`List` containing multiple `EnrichGT_obj` objects.
The `List` contains objects with overlapped enriched terms, unique enrich terms.
Details
Execute `obj.test` VS `obj.ctrl` tests, showing pathway overlaps (or differences) and meta-gene modules of test group and control group.
Supports ORA and GSEA results (enriched object or data.frame).
!WARNING!: `obj.test` and `obj.ctrl` should come from same database (e.g. GO Biological Process(GOBP)).