findIT_MARA {FindIT2} | R Documentation

## findIT_MARA

### Description

findIT_MARA

### Usage

    findIT_MARA(
      input_feature_id,
      peak_GR,
      peakScoreMt,
      TF_GR_database,
      log = TRUE,
      meanScale = TRUE,
      output = c("coef", "cor"),
      verbose = TRUE
    )

### 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.
`peakScoreMt` | peak count matrix.
`TF_GR_database` | TF peak GRange with a column named TF_id representing you TF name. If you have TF_score column, MARA will consider it. otherwise, MARA will consider each hit is 1.
`log` | whether you want to log your peakScoreMt
`meanScale` | whether you want to mean-centered per row
`output` | one of 'coef' and 'cor'. Default is coef
`verbose` | whether you want to report detailed running message

### Value

a data.frame

### Examples

    data("ATAC_normCount")
    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"

    set.seed(20160806)

    result_findIT_MARA <- findIT_MARA(
        input_feature_id = test_featureSet,
        peak_GR = peak_GR,
        peakScoreMt = ATAC_normCount,
        TF_GR_database = ChIP_peak_GR
    )

[Package FindIT2 version 1.0.3 Index]