Over-representation test of genes in each cluster
1 2 3 4 5 6 7 8 9 10 11 12 | compare_cluster_enrichment(
markers,
GO_data,
organism_db,
organism_name = "human",
logFC_term = "logFC",
pval_term = "padj",
gene_name = "feature",
log_FC_thres = 0.25,
pval_thres = 0.05,
enrich_area = "KEGG"
)
|
markers |
a dataframe of DE genes from Seurat; alternatively, a list of DE genes may be used |
GO_data |
result from go_data |
organism_db |
which organism database, for example, org.Hs.eg.db |
organism_name |
which organism for KEGG and Reactome, e.g. 'human'. If
|
logFC_term |
which column in |
enrich_area |
either KEGG or GO or reactome |
logFC_thres |
threshold of |
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