View source: R/3.enrichCluster.R
enrichCluster | R Documentation |
Perform GO/KEGG Enrichment Analysis for Multiple Clusters
enrichCluster(
object = NULL,
type = c("BP", "MF", "CC", "KEGG", "ownSet"),
TERM2GENE = NULL,
TERM2NAME = NULL,
OrgDb = NULL,
id.trans = TRUE,
fromType = "SYMBOL",
toType = c("ENTREZID"),
readable = TRUE,
organism = "hsa",
pvalueCutoff = 0.05,
topn = 5,
seed = 5201314,
add.gene = FALSE,
heatmap.type = c("plot_pseudotime_heatmap2", "plot_genes_branched_heatmap2",
"plot_multiple_branches_heatmap2"),
...
)
object |
An object containing clustering results.
This is clusterData object. Alternatively, it can be a |
type |
Character. The type of enrichment analysis to perform. Options include:
|
TERM2GENE |
A data frame containing mappings of terms to genes. Required when |
TERM2NAME |
A data frame containing term-to-name mappings. Optional when |
OrgDb |
An organism database object (e.g., |
id.trans |
Logical. Whether to perform gene ID transformation. Default is |
fromType |
Character. The type of the input gene IDs (e.g., |
toType |
Character. The target ID type for transformation using |
readable |
Logical. Whether to convert the enrichment result IDs back to a readable format (e.g., SYMBOL).
Only applicable for GO and KEGG analysis. Default is |
organism |
Character. The KEGG organism code (e.g., |
pvalueCutoff |
Numeric. The p-value cutoff for enriched terms to be included in the results. Default is |
topn |
Integer or vector. The number of top enrichment results to extract. If a single value, it is applied
to all clusters. Otherwise, it should match the number of clusters. Default is |
seed |
Numeric. Seed for random operations to ensure reproducibility. Default is |
add.gene |
Logical. Whether to include the list of genes associated with each enriched term in the results.
Default is |
heatmap.type |
Character. The type of heatmap visualization to use when input data is a
|
... |
Additional arguments passed to plot_pseudotime_heatmap2/plot_genes_branched_heatmap2/plot_multiple_branches_heatmap2 functions. |
a data.frame.
JunZhang
This function performs Gene Ontology (GO) or KEGG enrichment analysis, or custom gene set enrichment, on clustered genes. It supports multiple clusters, incorporating cluster-specific results into its analysis.
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