findIT_TFHit: findI(nfluential)T(F)_TFHit

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

findI(nfluential)T(F)_TFHit

Description

find influential TF of your input gene set based on TF ChIP-Seq or motif data

Usage

findIT_TFHit(
  input_genes,
  Txdb,
  TF_GR_database,
  scan_dist = 20000,
  decay_dist = 1000,
  Chrs_included,
  background_genes = NULL,
  background_number = 3000,
  verbose = TRUE
)

Arguments

input_genes	a character vector which represent genes set which you want to find influential TF for
Txdb	Txdb
TF_GR_database	TF peak GRange with a column named TF_id representing you TF name
scan_dist	scan distance
decay_dist	decay distance
Chrs_included	a character vector represent chromosomes which you want to sample background genes from
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

data.frame

Examples

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

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

    set.seed(20160806)
    result_findIT_TFHit <- findIT_TFHit(
        input_genes = test_geneSet,
        Txdb = Txdb,
        TF_GR_database = ChIP_peak_GR
    )

}

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