enhancerPromoterCor {FindIT2} | R Documentation

## enhancerPromoterCor

### Description

enhancerPromoterCor

### Usage

    enhancerPromoterCor(
      peak_GR,
      Txdb,
      up_scanPromoter = 500,
      down_scanPromoter = 500,
      up_scanEnhancer = 20000,
      down_scanEnhacner = 20000,
      peakScoreMt,
      parallel = FALSE,
      verbose = TRUE
    )

### Arguments

`peak_GR` | peak GRange with a column named feature_id representing you peak name
`Txdb` | Txdb
`up_scanPromoter` | the scan distance which is used to scan nearest promoter
`down_scanPromoter` | the scan distance which is used to scan nearest promoter
`up_scanEnhancer` | the scan distance which is used to scan feature
`down_scanEnhacner` | the scan distance which is used to scan feature
`peakScoreMt` | peak count matrix. The rownames are feature_id in peak_GR
`parallel` | whether you want to parallel to speed up
`verbose` | whether you want to report detailed running message

### Value

mmAnno with Cor, pvalue,padj,qvalue column

### Examples

    if (require(TxDb.Athaliana.BioMart.plantsmart28)){
        data("ATAC_normCount")
        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)[1:100]
        mm_ePLink <- enhancerPromoterCor(
        peak_GR = peak_GR,
        Txdb = Txdb,
        peakScoreMt = ATAC_normCount,
        parallel = FALSE)
    }

[Package FindIT2 version 1.0.3 Index]