run_GSEA_pairwise: Run pairwise GSEA

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

Run pairwise GSEA

Usage

run_GSEA_pairwise(
  markers,
  organism_db,
  save_path,
  group1 = NULL,
  group2 = NULL,
  group1_col = "group",
  group2_col = "compare_group",
  ...
)

Arguments

markers	a dataframe generated from find_DE_genes that contain the log fold change of gene expression.
organism_db	a gene database
group1	the cell types in group1. Upregulation of genes in this group will be reflected as positive enrichment.
group2	the cell types in group2. Upregulation here= negative enrichment
...	other arguments for run_GSEA_all_types. I strongly recommend checking the correct species by specifying organism_name=.... The default is human.

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