getTFtargets: Get TF target genes

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

This function uses ELMER analysis results and summarizes the possible genes targets for each TF

Usage

getTFtargets(
  pairs,
  enriched.motif,
  TF.result,
  dmc.analysis,
  mae,
  save = TRUE,
  dir.out = "./",
  classification = "family",
  cores = 1,
  label = NULL
)

Arguments

pairs	Output of get.pairs function: dataframe or file path
enriched.motif	List of probes for each enriched motif: list of file path. The file created by ELMER is getMotif...enriched.motifs.rda
TF.result	Output get.TF function: dataframe or file path
dmc.analysis	DMC results file or data frame
mae	A multiAssayExperiment outputed from createMAE function
save	A logic. If save is true, a files will be saved: getTFtarget.XX..csv If save is false, only a data frame contains the same content with the first file.
dir.out	A path specifies the directory for outputs of get.pair function. Default is current directory
classification	use family or subfamily classification to consider potential TF
cores	Number of cores to be used in parallel
label	A character labels the outputs.

Examples

pairs <- data.frame(Probe = c("cg26992600","cg26992800","cg26992900"),
                    Symbol = c("KEAP1","DSP","ATP86"))
enriched.motif <- list("FOXD3_HUMAN.H11MO.0.D"= c("cg26992800","cg26992900"))
TF.result <- data.frame(motif = c("FOXD3_HUMAN.H11MO.0.D"),
                        potential.TF.family = c("TP63;TP73"))
getTFtargets(pairs,enriched.motif,TF.result)

## Not run: 
getTFtargets("../LUAD_LUSC_analysis_hg38/hyper/getPair.hyper.pairs.significant.csv",
enriched.motif = "../LUAD_analysis_hg38/hyper/getMotif.hyper.enriched.motifs.rda",
TF.result = "../LUAD_analysis_hg38/hyper/getTF.hyper.significant.TFs.with.motif.summary.csv")

## End(Not run)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.