{GSEA} R# Documentation

GSEA

require(GCModeller);

#' The GCModeller GSEA toolkit
imports "GSEA" from "gseakit";

The GCModeller GSEA toolkit

Gene set enrichment analysis

Gene Set enrichment analysis (GSEA) (also called functional enrichment analysis Or pathway enrichment analysis) Is a method To identify classes Of genes Or proteins that are over-represented In a large Set Of genes Or proteins, And may have an association With disease phenotypes. The method uses statistical approaches To identify significantly enriched Or depleted groups Of genes. Transcriptomics technologies And proteomics results often identify thousands Of genes which are used For the analysis.

.NET clr type export
enrich: EnrichmentResult

The GCModeller enrichment analysis output table


.NET clr function exports
as.data.frame.enrichmentresult EnrichmentResult:

The GCModeller enrichment analysis output table
read.enrichment

Read the enrichment analysis result table from a csv file.
enrichment

do GSEA enrichment analysis

Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with disease phenotypes. The method uses statistical approaches to identify significantly enriched or depleted groups of genes. Transcriptomics technologies and proteomics results often identify thousands of genes which are used for the analysis.
fisher

Fisher exact test for the enrichment of a single gene set term.
enrichment.go

Do the GO (Gene Ontology) GSEA enrichment analysis.
write.enrichment

Save the enrichment analysis result as a csv table file.
as.KOBAS_terms

Convert GSEA enrichment result from GCModeller output format to KOBAS output format
enrichment.go_dag

Create the network graph data of the GO enrichment result for the Cytoscape.
enrichment.draw.go_dag

Draw the GO enrichment DAG graph as a raster image.
cast_enrichs

Create the GCModeller enrichment analysis result objects from the raw data vectors.
to_enrichment_terms

Cast a dataframe object into the CLR enrichment result objects.
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