findIT_regionRP: findI(nfluential)T(F)_regionRP

In shangguandong1996/FindIT2: find influential TF and Target based on multi-omics data

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
    )

}

shangguandong1996/FindIT2 documentation built on March 1, 2024, 8:34 p.m.