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Run GSEA using clusterProfiler::GSEA

run_gsea.Rd

This function is used to run a GSEA using the clusterProfiler::GSEA function.

Usage

run_gsea(
  ranked_gene_list,
  gene_sets,
  GSEA_p_val_thresh = 0.05,
  GSEA_minGSSize = 5,
  GSEA_maxGSSize = 500,
  my_seed = 1337L,
  ...
)

Arguments

ranked_gene_list

NAMED NUMERIC VECTOR : a numeric vector named by gene Entrez ID

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)

GSEA_p_val_thresh

NUMERIC : parameter to be passed to pvalueCutoff in clusterProfiler::GSEA function (default to 0.05)

GSEA_minGSSize

NUMERIC : parameter to be passed to minGSSize in clusterProfiler::GSEA function (default to 5)

GSEA_maxGSSize

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

my_seed

INTEGER : whether to set a seed or not, before running clusterProfiler::GSEA. Set NULL to not set seed (default to 1337L)

...

other parameters to be passed to clusterProfiler::GSEA function

Value

The output of clusterProfiler::GSEA function. One can use @result slot and run aquarius::gsea_plot function. One can use the clusterProfiler::gseaplot to plot GSEA famous figure