compare_enrich: compare_enrich

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

compare_enrich

Description

Function to run over representation analysis on your hits and return a plot that compare the pathways found between your treatments.

Usage

compare_enrich(
  hits,
  gene_column = "Gene",
  treatment_column = NULL,
  species = c("human", "mouse"),
  n_pathway = 5,
  pval_cutoff = 0.01,
  minGSSize = 3,
  database = c("WikiPathway", "KEGG", "GO", "CETSA")
)

Arguments

hits	The hitlist; a data.frame containing the genes id and preferably a treatment column but not necessary.
gene_column	The name of the coulumn that contains the genes. Default is 'Gene'.
treatment_column	The name of the column that contains the treatments. Default is NULL.
species	Specify the species. Currently, only 'human' and 'mouse' are available.
n_pathway	Number of pathway to show on plot. Default is 5. For more info you, see compareCluster.
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.