run_GSEA_all_types: Combine the GSEA results from all clusters

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

Combine the GSEA results from all clusters

Usage

run_GSEA_all_types(
  markers,
  organism_db,
  organism_name = "human",
  show_num = 50,
  cluster_col = "group",
  enrich_area = "KEGG",
  save_path = NULL,
  AP = NULL,
  ...
)

Arguments

markers	a dataframe containing the fold changes of genes with a column specified as cluster_col that contains the cluster information
organism_db	which organism database, for example, org.Hs.eg.db
show_num	how many GO/KEGG terms to show. This function will select those terms whose mean absolute fold changes are high
enrich_area	either 'GO', 'KEGG' or 'reactome'
save_path	save the GSEA results for later usage. GSEA is quite computationally intensive, especially considering that it will be run for all clusters

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.