run_gsea: run_gsea

In mgerault/mineCETSAapp: A shiny app for IMPRINTS.CETSA package

run_gsea

Description

Function to run gene set enrichment analysis and plot a GSEA plot.

Usage

run_gsea(
  hits,
  gene_column = "Gene",
  score_column = "IS",
  treatment_column = NULL,
  treatment = NULL,
  species = c("human", "mouse"),
  pos_enrichment = TRUE,
  pval_cutoff = 0.01,
  minGSSize = 3,
  database = c("WikiPathway", "KEGG", "GO", "CETSA")
)

Arguments

hits	A data.frame containing the genes id, a score value and preferably a treatment column but not necessary.
gene_column	The name of the column that contains the genes. Default is 'Gene'.
score_column	The name of the column that contains the score values. Default is 'IS'.
treatment_column	The name of the column that contains the treatments. Default is NULL.
treatment	The name of the treatment you want to keep. Default is NULL.
species	Specify the species. Currently, only 'human' and 'mouse' are available.
pos_enrichment	Logical to tell if you want to only look at positive enrichment score. If FALSE, show only negative.
pval_cutoff	The p-value cutoff for the enrichment analysis.
minGSSize	minimal size of each gene set for analyzing. default here is 3
database	Specify the database. Currently, WikiPathway, KEGG, GO and CETSA are available.

Value

A list that contains the results and the plot.

See Also

clusterProfiler

mgerault/mineCETSAapp documentation built on April 17, 2025, 7:24 p.m.