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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)).

Author

Zhiming Ye