getTFtargets {ELMER} | R Documentation

## Get TF target genes

### 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)

[Package ELMER version 2.16.0 Index]