enriched_pathways: returns pathways from enrichR

In KatrionaGoldmann/omicAnnotations: Use databases to annotate genomic and transcriptomic data

returns pathways from enrichR

Description

returns pathways from enrichR

Usage

enriched_pathways(
  genes,
  drop_terms = c("User", "Enrichr"),
  keep_terms = c(),
  dbs = NULL,
  cutoff = 0.05,
  min_N = 2,
  remove_old = TRUE,
  libraries = c("Transcription", "Pathways"),
  plot_cap = 20,
  plot_pcutoff = 0.01,
  plot_colour = "Combined.Score",
  plot_x = "P.value",
  plot_vline = NA,
  check_for_updates = TRUE
)

Arguments

genes	List of gene names
drop_terms	terms in databases not to search. If NULL only keep_terms used
keep_terms	terms in databases to search. If NULL only all except drop_terms used
dbs	database of enrichR pathways. If NULL all are selected minus those removed by drop_terms. See listEnrichrDbs().
cutoff	pvalue cutoff
min_N	minimum number of genes to consider
remove_old	Whether to remove legacy libraries ()
libraries	Which type of libraries to check for enrichment. Options include c('Transcription', 'Pathways', 'Ontologies', 'Diseases_Drugs', 'Cell_Types', 'Misc'))
plot_cap	Maximum number of terms to plot
plot_pcutoff	Pvalue cutoff for plotting
plot_colour	Parameter for the colour scaling
plot_x	Parameter to plot on the x-axis
plot_vline	Position for vertical line
check_for_updates	Whether to check for updates in the enrichR database

KatrionaGoldmann/omicAnnotations documentation built on June 23, 2022, 2:15 p.m.