compare_cluster_enrichment: Over-representation test of genes in each cluster

Description Usage Arguments

Description

Over-representation test of genes in each cluster

Usage

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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"
)

Arguments

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 enrich_area is TF or MIRNA, the organism name should be for the gprofiler database, e.g. 'hsapiens', 'mmusculus'

logFC_term

which column in markers contains the information for ranking gene expression

enrich_area

either KEGG or GO or reactome

logFC_thres

threshold of logFC_term beyond which a gene is selected for over-representation test


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