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clusterProfiler::enricher wrapper

run_enrichr.Rd

This function is a wrapper around clusterProfiler::enricher function

Usage

run_enrichr(
  gene_names,
  gene_corresp,
  gene_sets,
  make_plot = TRUE,
  plot_title = "",
  plot_n_cat = 30,
  FE_pAdjustMethod = "BH",
  FE_pvalueCutoff = 0.01,
  FE_qvalueCutoff = 0.05,
  minGSSize = 10,
  maxGSSize = 500,
  ...
)

Arguments

gene_names

CHARACTER VECTOR : a vector containing gene names (no default)

gene_corresp

DATAFRAME : a dataframe with at least two columns :

  • NAME contains gene names

  • ID contains associated ID (Entrez ID, Ensembl ID...) Use aquarius::get_gene_id function to build such a dataframe (no default)

gene_sets

DATAFRAME : a dataframe with at least two columns

  • gs_name contains the gene set name

  • ID contains genes ID (Entrez ID, Ensembl ID...) Use aquarius::get_gene_sets function to build such a dataframe (no default)

make_plot

LOGICAL : whether to build dotplot using clusterProfiler::dotplot or not (default to TRUE)

plot_title

CHARACTER : plot title, only used if make_plot is TRUE (default to "")

plot_n_cat

INTEGER : parameter to be passed to showCategory in clusterProfiler::dotplot function (default to 30)

FE_pAdjustMethod

: parameter to be passed to pAdjustMethod in clusterProfiler::enricher function (default to "BH")

FE_pvalueCutoff

: parameter to be passed to pvalueCutoff in clusterProfiler::enricher function (default to 0.01)

FE_qvalueCutoff

: parameter to be passed to qvalueCutoff in clusterProfiler::enricher function (default to 0.05)

minGSSize

: parameter to be passed to minGSSize in clusterProfiler::enricher function (default to 10)

maxGSSize

: parameter to be passed to maxGSSize in clusterProfiler::enricher function (default to 500)

...

other parameters to be passed to clusterProfiler::enricher function

Value

The output :

  • make_plot == TRUE : a list containing enrichr output and the plot

  • make_plot == FALSE : clusterProfiler::enricher output only