createHTMLReport: Make GO-Term analysis and print out Report

In paulklemm/mygo: Create Report for mus musculus dataset of GO-term analysis using clusterProfiler

Make GO-Term analysis and print out Report

Description

Make GO-Term analysis and print out Report

Usage

createHTMLReport(
  dat,
  output_path,
  save_excel = TRUE,
  significance_cutoff = 0.05,
  do_gse = TRUE,
  simplify_ontologies = TRUE,
  use_background = TRUE,
  store_r_objects = TRUE,
  simplify_cutoff = 0.7,
  save_plots_as_pdf = TRUE
)

Arguments

dat	Dataframe containing variables q_value and EntrezID or EnsemblID
output_path	Path to HTML output
save_excel	Save GO-terms to Excel files
significance_cutoff	Specify the cutoff which entries are considered significant
do_gse	Conduct GSE analysis
simplify_ontologies	Run time-consuming ontology simplification
use_background	Use background genes for the analysis
store_r_objects	Store clusterProfiler R objects as compressed RDS files to output_path
simplify_cutoff	See clusterProfiler::simplify
save_plots_as_pdf	Export all plots as PDF to output_path/plots

Value

cummeRbund cuff object

paulklemm/mygo documentation built on July 27, 2023, 11:36 a.m.