findIT_enrichWilcox {FindIT2} | R Documentation

## findIT_enrichWilcox

### Description

findIT_enrichWilcox

### Usage

    findIT_enrichWilcox(
      input_feature_id,
      peak_GR,
      TF_GR_database,
      background_peaks = NULL,
      background_number = 3000
    )

### Arguments

`input_feature_id` | a character vector which represent peaks set which you want to find influential TF for
`peak_GR` | a GRange object represent your whole feature location with a column named feature_id, which your input_feature_id should a part of it.
`TF_GR_database` | TF peak GRange with a column named TF_id representing you TF name
`background_peaks` | a character vector which represent background peak set. If you do not assign background peaks, program will sample background_number peaks as background peaks from all feature_id in your peak_GR
`background_number` | background peaks number

### Value

data.frame

### Examples

    data("test_featureSet")
    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"

    result_findIT_enrichWilcox <- findIT_enrichWilcox(
        input_feature_id = test_featureSet,
        peak_GR = peak_GR,
        TF_GR_database = ChIP_peak_GR
    )

[Package FindIT2 version 1.0.3 Index]