gene_concept_net: gene_concept_net

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

gene_concept_net

Description

Function to run over representation analysis on your hits and return a network plot.

Usage

gene_concept_net(
  hits,
  gene_column = "Gene",
  score_column = "IS",
  treatment_column = NULL,
  treatment = NULL,
  species = c("human", "mouse"),
  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 ant to keep. Default is NULL.
species	Specify the species. Currently, only 'human' and 'mouse' are available.
pval_cutoff	The p-value cutoff for the gene concept network.
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

The gene concept network plot.

See Also

clusterProfiler

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