calcRP_coverage {FindIT2} | R Documentation

## calcRP_coverage

### Description

calculate regulatory potential using big wig files, which is useful for ATAC or H3K27ac histone modification data.

### Usage

    calcRP_coverage(
      bwFile,
      Txdb,
      gene_included,
      Chrs_included,
      decay_dist = 1000,
      scan_dist = 20000,
      verbose = TRUE
    )

### Arguments

`bwFile` | bw file
`Txdb` | Txdb
`gene_included` | a character vector which represent gene set which you want to calculate RP for
`Chrs_included` | a character vector which represent chromosomes where you want to calculate gene RP in
`decay_dist` | decay distance
`scan_dist` | scan distance
`verbose` | whether you want to report detailed running message

### Details

Please note that because of rtracklayer::import has some issue on 32 bit R of windows, so the calcRP_coverage can not work on this system. But if your R is 64 bit, which now be applied on the most windows R, this function still work.

### Value

data.frame

### Examples

    if (.Platform$OS.type != "windows" & require(TxDb.Athaliana.BioMart.plantsmart28)) {
        Txdb <- TxDb.Athaliana.BioMart.plantsmart28
        seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))
        bwFile <- system.file("extdata", "E50h_sampleChr5.bw", package = "FindIT2")

        RP_df <- calcRP_coverage(
            bwFile = bwFile,
            Txdb = Txdb,
            Chrs_included = "Chr5"
        )

    }

[Package FindIT2 version 1.0.3 Index]