Performs gene enrichment analysis using either traditional over-representation analysis (GO/KEGG) or Gene Set Enrichment Analysis (GSEA). Supports both human and mouse organisms.
Usage
GeneEnrichment(
STID_obj = NULL,
up_gene = NULL,
down_gene = NULL,
DEGs = NULL,
host_org = NULL,
method = "GO_KEGG",
plot_pathway_num = 12,
internal = FALSE,
col = viridis(100, option = "H")[15:85] %>% rev(),
return_data = FALSE,
grp_nm = NULL,
dir_nm = "M3_GeneEnrichment",
...
)Arguments
- STID_obj
STID object (optional, used to extract host organism)
- up_gene
Character vector, upregulated genes for GO/KEGG analysis
- down_gene
Character vector, downregulated genes for GO/KEGG analysis
- DEGs
Data frame, differential expression results with columns 'SYMBOL' and 'LogFC' for GSEA analysis
- host_org
Character, host organism - "human" or "mouse" (if NULL, extracted from STID_obj)
- method
Character, method to use - "GO_KEGG" or "GSEA_GO_KEGG" (default: "GO_KEGG")
- plot_pathway_num
Integer, number of top pathways to display in plots (default: 12)
- internal
Logical, whether to use internal KEGG database (default: FALSE)
- col
Color palette for plots (default:
viridis(100, option = "H")[15:85] %>% rev())- return_data
Logical, whether to return enrichment results (default: FALSE)
- grp_nm
Character, group name for output organization (default: NULL)
- dir_nm
Character, directory name for output (default: "M3_GeneEnrichment")
- ...
Additional arguments passed to internal functions
Examples
if (FALSE) { # \dontrun{
# GO/KEGG enrichment with up and down regulated genes
GeneEnrichment(
up_gene = upregulated_genes,
down_gene = downregulated_genes,
host_org = "human",
plot_pathway_num = 10
)
# GSEA enrichment with DEGs
GeneEnrichment(
DEGs = deg_results,
host_org = "mouse",
method = "GSEA_GO_KEGG"
)
} # }