plot_enrichment: Generate enrichment analysis plots

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

Generate enrichment analysis plots

Description

This function runs KEGG and GO enrichment analysis of peak files and generates dot plots.

Usage

plot_enrichment(
  peaklist,
  txdb = NULL,
  tss_distance = c(-3000, 3000),
  pvalueCutoff = 0.05,
  interact = FALSE,
  verbose = TRUE
)

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.
pvalueCutoff	P-value cutoff, passed to compareCluster.
interact	Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.
verbose	Print messages.

Value

KEGG and GO dot plots

Examples

### Load Data ###
data("CnT_H3K27ac") # example peakfile GRanges object
data("CnR_H3K27ac") # example peakfile GRanges object 
### Create Named Peaklist ###
peaklist <- list("CnT"=CnT_H3K27ac, "CnR"=CnR_H3K27ac) 
enrich_res <- plot_enrichment(peaklist = peaklist, pvalueCutoff=1,
                              tss_distance = c(-50,50)) 

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