calcRP_region {FindIT2} | R Documentation

## calcRP_region

### Description

calculate regulatory potential based on mm_geneScan result and peakCount matrix, which is useful for ATAC or H3K27ac histone modification data.

### Usage

    calcRP_region(
      mmAnno,
      peakScoreMt,
      Txdb,
      Chrs_included,
      decay_dist = 1000,
      log_transform = FALSE,
      verbose = TRUE
    )

### Arguments

`mmAnno` | the annotated GRange object from mm_geneScan
`peakScoreMt` | peak count matrix. The rownames are feature_id in mmAnno, while the colnames are sample names
`Txdb` | Txdb
`Chrs_included` | a character vector which represent chromosome where you want to calculate gene RP in. If Chromosome is not be set, it will calculate gene RP in all chromosomes in Txdb.
`decay_dist` | decay distance
`log_transform` | whether you want to log and norm your RP
`verbose` | whether you want to report detailed running message

### Value

a MultiAssayExperiment object containg detailed peak-RP-gene relationship and sumRP info

### Examples

    if (require(TxDb.Athaliana.BioMart.plantsmart28)) {
        data("ATAC_normCount")
        library(SummarizedExperiment)
        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)
        mmAnno <- mm_geneScan(peak_GR, Txdb)

        regionRP <- calcRP_region(
            mmAnno = mmAnno,
            peakScoreMt = ATAC_normCount,
            Txdb = Txdb,
            Chrs_included = "Chr5"
        )

        sumRP <- assays(regionRP)$sumRP
        fullRP <- assays(regionRP)$fullRP
    }

[Package FindIT2 version 1.0.3 Index]