Perform Gene Set Enrichment Analysis and plot it.
create_gsea_report_level.RdThis function conducts a Gene Set Enrichment Analysis (GSEA) using either the clusterProfiler package. Afterwards, it plots the results. It allows for customization of enrichment parameters, selection of databases, and optionally specifying a custom plot title and background gene list.
Usage
create_gsea_report_level(
clustered_genes,
databases,
params = NA,
plot_title = "",
universe = NULL
)Arguments
- clustered_genes
A list of dataframes with two columns: the first column contains the standard gene symbol, and the second column contains an integer specifying the cluster.
- databases
A dataframe containing the data of the downloaded Enrichr databases
- params
A list specifying the clusterProfiler parameters for the enrichment analysis.
- plot_title
An optional string specifying the title of the plot. If not provided, a default title based on the analysis will be used.
- universe
An optional list of standard gene symbols to be used as the background for the enrichment analysis instead of the background chosen by the `enricher`. The default is an empty list, which implies the use of the default background set by the enrichment tool.