findIT_regionRP {FindIT2} | R Documentation

## findI(nfluential)T(F)_regionRP

### Description

find Influential TF of your input gene set based on regulatory potential data and TF ChIP-Seq or motif data

### Usage

    findIT_regionRP(
      regionRP,
      Txdb,
      TF_GR_database,
      input_genes,
      background_genes = NULL,
      background_number = 3000,
      verbose = TRUE
    )

### Arguments

`regionRP` | the MultiAssayExperiment object from calcRP_region
`Txdb` | Txdb
`TF_GR_database` | TF peak GRange with a column named TF_id representing you TF name
`input_genes` | a character vector which represent genes set which you want to find influential TF for
`background_genes` | a character vector which represent background genes set. If you do not assign background gene , program will sample background_number genes as background genes from all gene sets.
`background_number` | background genes number
`verbose` | whether you want to report detailed running message

### Value

a MultiAssayExperiment object containg detailed TF-percent and TF-pvalue

### Examples

    if (require(TxDb.Athaliana.BioMart.plantsmart28)) {
        data("ATAC_normCount")
        data("test_geneSet")
        Txdb <- TxDb.Athaliana.BioMart.plantsmart28
        seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))

        peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2")
        peak_GR <- loadPeakFile(peak_path)

        ChIP_peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2")
        ChIP_peak_GR <- loadPeakFile(ChIP_peak_path)
        ChIP_peak_GR$TF_id <- "AT1G28300"

        mmAnno <- mm_geneScan(peak_GR, Txdb)

        regionRP <- calcRP_region(
            mmAnno = mmAnno,
            peakScoreMt = ATAC_normCount,
            Txdb = Txdb,
            Chrs_included = "Chr5"
        )

        set.seed(20160806)
        result_findIT_regionRP <- findIT_regionRP(
            regionRP = regionRP,
            Txdb = Txdb,
            TF_GR_database = ChIP_peak_GR,
            input_genes = test_geneSet,
            background_number = 3000
        )

    }

[Package FindIT2 version 1.0.3 Index]