Identify TFs from Gene Expression Reults.

Identify TFs from Gene Expression Reults.

InferRegulator(
  genes,
  control.genes,
  method = c("ChEA3", "BART2", "TFEA.ChIP"),
  species = c("Human", "Mouse"),
  projet.name = NULL,
  library = c("meanRank", "topRank", "GTEx", "ReMap", "Enrichr", "ENCODE", "ARCHS4",
    "Literature"),
  bart2.path = NULL,
  filter.threshold = NULL
)

Arguments

genes	Input genes, can be a set of differentially expressed genes. When method is "ChEA3" or "BART2", the genes should be SYMBOL of human or mouse. When method is "TFEA.ChIP", the genes can be SYMBOL/ENSEMBL/ENTREZ of human.
control.genes	Input genes of human, can be a set of non-differentially expressed genes. Used when method is "TFEA.ChIP".
method	The method used to identify TFs, choose from "ChEA3", "BART2", "TFEA.ChIP". Default: "ChEA3".
species	The species of input gene set. Choose from "Human" and "Mouse" when method is "ChEA3" or "BART2", "Human" when method is "TFEA.ChIP". Default: "Human".
projet.name	The name of the project used as Query Name. Default: NULL (DEbPeak).
library	The output library type, choose from "meanRank", "topRank", "GTEx", "ReMap", "Enrichr", "ENCODE", "ARCHS4", "Literature". Used when method is "ChEA3". Default: "meanRank".
bart2.path	BART2 path. Default: NULL (conduct automatic detection).
filter.threshold	The threshold used to filter the results. When method is "ChEA3", filter on Score column. When method is "BART2", filter on pvalue column. When method is "TFEA.ChIP", filter on pVal column.

Value

Dataframe contains identified TFs.

Examples

# library(DEbPeak)
# InferRegulator(genes = c("SMAD9","FOXO1","MYC","STAT1",'STAT3',"SMAD3"), method = "ChEA3", species = "Human")