extracts transcription factor (TF) and target gene (TG) information

This function extracts information about transcription factor (TF) and target gene (TG) with TFactS Catalogue (v2).

extractTFTG(
  DEGs,
  catalog,
  TF.col = "TF..OFFICIAL_TF_CODING_GENE_NAME.",
  TG.col = "Target.gene..OFFICIAL_GENE_NAME."
)

Arguments

DEGs

a character vector of DEGs (differentially expressed genes)

catalog

a data frame of TFactS catalog (ver. 2)

TF.col

the name of the column that contains the TF names

TG.col

the name of the column that contains the TG names

Value

list

Author

Atsushi Fukushima

Examples

data(DEGs)
data(catalog)

res <- extractTFTG(DEGs, catalog)
head(res$TFs)
#> [1] "ATF4"   "BCL6"   "CREB1"  "CTNNB1" "ETS1"   "FLI1"