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Infering Pathway or Transcript Factors activity from EnrichGT meta-gene modules

infering_regulator_act.Rd

Only supports gene symbols. so you must use enrichedObj |> setReadable(OrgDb = xxx,keyType = "ENTREZID") |> EnrichGT() . Do Not supports ENTREZIDs!

[PROGENy](https://saezlab.github.io/progeny/) is a comprehensive resource containing a curated collection of pathways and their target genes, with weights for each interaction.

[CollecTRI](https://github.com/saezlab/CollecTRI) is a comprehensive resource containing a curated collection of TFs and their transcriptional targets compiled from 12 different resources. This collection provides an increased coverage of transcription factors and a superior performance in identifying perturbed TFs compared to our previous.

Usage

infering_regulator_act(x, DB = "collectri", species = "human")

Arguments

x

an EnrichGT_obj object.

DB

can be "progeny" (the Pathway activity database), or "collectri" (TF activity database)

species

can be "human" or "mouse"

Value

a `compareCluster` result from `clusterProfiler`

Author

Zhiming Ye, Saez-Rodriguez Lab (The decoupleR package, https://saezlab.github.io/decoupleR/)