mm_nearestGene: mm_nearestGene

View source: R/mmPeakAnno.R

mm_nearestGeneR Documentation

mm_nearestGene

Description

Annotate peaks using nearest gene mode, which means every peak only have one related gene.

Usage

mm_nearestGene(peak_GR, Txdb, reportGeneInfo = FALSE, verbose = TRUE, ...)

Arguments

peak_GR

peak GRange with a column named feature_id representing you peak name

Txdb

Txdb

reportGeneInfo

whether you want to report full gene info

verbose

whether you want to report detailed running message

...

additional arguments in distanceToNearest

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_nearestGene(peak_GR, Txdb)
    peakAnno
}

shangguandong1996/FindIT2 documentation built on March 1, 2024, 8:34 p.m.