mm_geneBound: mm_geneBound

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

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
}

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