mm_geneScan {FindIT2} | R Documentation

## mm_geneScan

### Description

Annotate peaks using geneScan mode, which means every peak have more than one related genes.

### Usage

    mm_geneScan(
      peak_GR,
      Txdb,
      upstream = 3000,
      downstream = 3000,
      reportGeneInfo = FALSE,
      verbose = TRUE,
      ...
    )

### Arguments

`peak_GR` | peak GRange with a column named feature_id representing you peak name
`Txdb` | Txdb
`upstream` | distance to start site(upstream)
`downstream` | distance to start site(downstream)
`reportGeneInfo` | whether you want to add gene info
`verbose` | whether you want to report detailed running message
`...` | additional arguments in findOverlaps

### Value

Granges object with annotated info

### 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)
        peakAnno <- mm_geneScan(peak_GR, Txdb)
        peakAnno
    }

[Package FindIT2 version 1.0.3 Index]