plot_ChIPseeker_annotation: Create ChIPseeker annotation plot

In neurogenomics/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

Create ChIPseeker annotation plot

Description

This function annotates peaks using ChIPseeker::annotatePeak. It outputs functional annotation of each peak file in a barplot.

Usage

plot_ChIPseeker_annotation(
  peaklist,
  txdb = NULL,
  tss_distance = c(-3000, 3000),
  interact = FALSE
)

Arguments

peaklist	A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2). If not named, default file names will be assigned.
txdb	A TxDb annotation object from Bioconductor.
tss_distance	A vector specifying the distance upstream and downstream around transcription start sites (TSS). The default value is c(-3000,3000); meaning peak frequency 3000bp upstream and downstream of TSS will be displayed.
interact	Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

Value

ggplot barplot

Examples

### Load Data ###
data("CnT_H3K27ac") # example peakfile GRanges object
data("CnR_H3K27ac") # example peakfile GRanges object 
peaklist <- list("CnT"=CnT_H3K27ac, "CnR"=CnR_H3K27ac)
my_plot <- plot_ChIPseeker_annotation(peaklist = peaklist, 
                                      tss_distance = c(-50,50))

neurogenomics/EpiCompare documentation built on Oct. 18, 2024, 11:04 p.m.