calculateEnrichmentTest: performs enrichment analysis

In TFactSR: Enrichment Approach to Predict Which Transcription Factors are Regulated

performs enrichment analysis

Description

This function performs enrichment test (ET) based on Fisher's exact test

Usage

calculateEnrichmentTest(
  DEGs,
  catalog,
  TFs,
  TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME."
)

Arguments

DEGs	a character vector of DEGs (differentially expressed genes)
catalog	a data frame of TFactS catalog (ver. 2)
TFs	a character vector of transcription factor
TF.col	the name of the column that contains the TF names

Value

data.frame

Author(s)

Atsushi Fukushima Definition: m is the number of target genes annotated for the TF under consideration n is the number of query genes N is the number of regulations in the catalog k is the number of query genes that are annotated as regulated by TF (i.e., the intersection between the query and the TF signature)

References

Essaghir A et al. Nucleic Acids Res. 2010 Jun;38(11):e120.

Examples

data(DEGs)
data(catalog)

tftg <- extractTFTG(DEGs, catalog)
TFs <- tftg$TFs

res <- calculateEnrichmentTest(DEGs, catalog, TFs)

TFactSR documentation built on Aug. 31, 2023, 5:09 p.m.