find_impacted_pathways: Functional enrichment analysis

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Functional enrichment analysis

Description

Performs gene ontology and impacted pathway enrichment analysis with a list of gene names and their fold-change.

Usage

find_impacted_pathways(
  gene_file = NULL,
  reference_file = NULL,
  organism = c("hsapiens"),
  enrichment_tool = c("WebGestaltR", "enrichR"),
  enrichment_database = c("GO_Biological_Process", "GO_Cellular_Component",
    "GO_Molecular_Function", "KEGG", "Reactome", "Wikipathway"),
  ...
)

Arguments

gene_file	A data frame or the path of a .tsv file containing a list of genes, their fold-change, p-value and adjusted p-value. Column names should be gene, logFC, pval and padj respectively.
reference_file	A data frame containing all the genes that were used as input for differential expression. Column name should be gene. If not provided the human protein-coding genome will be used as background genes.
organism	Organism name. hsapiens for Homo sapiens, mmusculus for Mus musculus
enrichment_tool	Enrichment tool to use. WebGestaltR and enrichR is implemented. Use one or more of the tools.
enrichment_database	Name of the database for enrichment. User can specify one or more database names. Check list_databases() for available database alias.
...	Additional arguments

Value

enrichment_result a list of list containing enrichment outputs from different enrichment tools.

See Also

Other Impacted pathway analysis: list_databases(), pathway_analysis_enrichr(), pathway_analysis_webgestaltr(), report_impacted_pathway()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.