mm_nearestGene: mm_nearestGene

In shangguandong1996/FindIT2: find influential TF and Target based on multi-omics data

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.