calcRP_TFHit {FindIT2} | R Documentation

## calcRP_TFHit

### Description

calculate regulatory potential based on ChIP-Seq peak data, which is useful for TF ChIP-seq data.

### Usage

    calcRP_TFHit(
      mmAnno,
      Txdb,
      decay_dist = 1000,
      report_fullInfo = FALSE,
      verbose = TRUE
    )

### Arguments

`mmAnno` | the annotated GRange object from mm_geneScan
`Txdb` | Txdb
`decay_dist` | decay distance
`report_fullInfo` | whether you want to report full peak-RP-gene info
`verbose` | whether you want to report detailed running message

### Details

If your origin peak_GR of mmAnno have column named feature_score, calcRP_TFHit will consider this column when calculating sumRP. Otherwise, it will consider all peak Hit feature_score is 1.

### Value

if report_fullInfo is TRUE, it will output GRanges with detailed info. While FALSE, it will output data frame

### Examples

    if (require(TxDb.Athaliana.BioMart.plantsmart28)){
        Txdb <- TxDb.Athaliana.BioMart.plantsmart28
        seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))
        peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2")
        peak_GR <- loadPeakFile(peak_path)
        mmAnno <- mm_geneScan(peak_GR, Txdb)

        # if you just want to get RP_df, you can set report_fullInfo FALSE
        fullRP_hit <- calcRP_TFHit(
            mmAnno = mmAnno,
            Txdb = Txdb,
            report_fullInfo = TRUE
        )

        RP_df <- metadata(fullRP_hit)$peakRP_gene

    }

[Package FindIT2 version 1.0.3 Index]