Functional enrichment analysis using WebgestaltR

Source: R/pathway_analysis_webgestaltr.R

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

pathway_analysis_webgestaltr(
  gene_file = NULL,
  reference_file = NULL,
  organism = getOption("scflow_species", default = "human"),
  enrichment_method = "ORA",
  enrichment_database = c("geneontology_Biological_Process_noRedundant",
    "geneontology_Cellular_Component_noRedundant",
    "geneontology_Molecular_Function_noRedundant", "pathway_KEGG", "pathway_Reactome",
    "pathway_Wikipathway")
)

Arguments

gene_file

For ORA, A data frame containing a list of significant genes with column name gene or a vector of significant genes. For GSEA a data frame containing a list of all genes in the analysis, 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

default is human. From WebGestaltR supports 12 organisms, common choices are "hsapiens" or "mmusculus". Users can use the function WebGestaltR::listOrganism() to check available organisms. Users can also input others to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.

enrichment_method

Method of enrichment analysis. Either over-representation analysis (ORA) or (Gene set enrichment analysis) GSEA.

enrichment_database

Name of the database for enrichment. If not provided then multiple databases will be used or user can specify one or more database names from WebGestaltR::listGeneSet()

Value

enrichment_result a list of data.frames containing enrichment output and a list of plots of top 10 significant genesets.

See also

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