mm_geneBound {FindIT2} | R Documentation

## mm_geneBound

### Description

find related peaks of your input genes, which is useful when you want to plot volcano plot or heatmap of peaks.

### Usage

    mm_geneBound(peak_GR, Txdb, input_genes, verbose = TRUE, ...)

### Arguments

`peak_GR` | peak GRange with a column named feature_id representing you peak name
`Txdb` | Txdb
`input_genes` | a character vector which represent genes set which you want to find related peak for
`verbose` | whether you want to report detailed running message
`...` | additional arguments in distanceToNearest

### Value

data.frame with three column: related peak id, your input gene id, and distance

### 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)
        peak_pair <- mm_geneBound(peak_GR, Txdb, c("AT5G01015", "AT5G67570"))
        peak_pair
    }

[Package FindIT2 version 1.0.3 Index]