pathway_enrich | R Documentation |
Performs over‐representation testing via DOSE/clusterProfiler against KEGG or custom gene sets.
pathway_enrich(
gene,
organism = "ppu",
keyType = "kegg",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe,
minGSSize = 10,
maxGSSize = 500,
qvalueCutoff = 0.2,
use_internal_kegg = FALSE,
custom_gene_sets = FALSE,
custom_pathways = NULL
)
gene |
Character vector of gene or protein IDs to test for enrichment. |
organism |
KEGG organism code (e.g. |
keyType |
ID type (default |
pvalueCutoff |
Numeric; p‐value cutoff (default |
pAdjustMethod |
Character; adjustment method (default |
universe |
Character vector of background IDs. |
minGSSize |
Integer; minimum gene set size. |
maxGSSize |
Integer; maximum gene set size. |
qvalueCutoff |
Numeric; q‐value cutoff (default |
use_internal_kegg |
Logical; use internal KEGG DB if |
custom_gene_sets |
Logical; use custom gene sets if |
custom_pathways |
Data frame with columns |
An enrichResult
object (or NULL
if no pathways pass the thresholds).
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