plot_annoDistance: plot_annoDistance

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

plot_annoDistance

Description

plot the distance distribution of mmAnno from mm_nearestGene, which helps you decide whehter your TF is promoter or enhancer dominant

Usage

plot_annoDistance(mmAnno, quantile = c(0.01, 0.99))

Arguments

mmAnno	the annotated GRange object from mm_nearestGene
quantile	the quantile of distanceToTSS you want to show

Value

a ggplot2 object

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)
    plot_annoDistance(peakAnno)

}

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