PEI
(Package: cogena) :
Significance of Gene sets enrichment.
Caculating the significance of Gene sets enrichment based on the hypergeometric test. This function is mainly used internally.
● Data Source:
BioConductor
● Keywords:
● Alias: PEI
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clEnrich
(Package: cogena) :
Gene set enrichment for clusters
Gene set enrichment for clusters sourced from coExp function. the enrichment score are based on -log2(p) with p from hyper-geometric test.
● Data Source:
BioConductor
● Keywords:
● Alias: clEnrich
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clEnrich_one
(Package: cogena) :
Gene set enrichment for clusters (for one clustering method and a certain
Gene set enrichment for clusters sourced from coExp function. the enrichment score are based on -log(p) with p from hyper-geometric test.
● Data Source:
BioConductor
● Keywords:
● Alias: clEnrich_one
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clusterMethods
(Package: cogena) :
Basic methods for a genecl object.
clusterMethods: get the methods of clustering used.
● Data Source:
BioConductor
● Keywords:
● Alias: clusterMethods, clusterMethods,cogena-method, clusterMethods,cogena_methods, clusterMethods,genecl-method, clusterMethods,genecl_methods
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coExp
(Package: cogena) :
co-expressed gene-set enrichment analysis
Co-expressed gene-set enrichment analysis. Gene sets could be Pathway, Gene ontology. The gene co-expression is obtained by various clustering methods.
● Data Source:
BioConductor
● Keywords:
● Alias: coExp
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cogena-class
(Package: cogena) :
An S4 class to represent co-expressed gene-set enrichment
An S4 class to represent co-expressed gene-set enrichment analysis result.
● Data Source:
BioConductor
● Keywords:
● Alias: cogena-class
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cogena_package
(Package: cogena) :
Co-expressed gene set enrichment analysis
To discovery smaller scale, but highly correlated cellular events that may be of great biological relevance, co-expressed gene set enrichment analysis, cogena, clusters gene expression profiles (coExp) and then make enrichment analysis for each clusters (clEnrich) based on hyper-geometric test. The heatmapCluster and heatmapPEI can visualise the results. See vignette for the detailed workflow.
● Data Source:
BioConductor
● Keywords: package
● Alias: cogean_package, cogena, cogena_package, cogena_package-package
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corInCluster
(Package: cogena) :
Correlation in the cluster of a cogena object
Correlation in the cluster of a cogena object. This is helpful if the number of genes in cluster are small.
● Data Source:
BioConductor
● Keywords:
● Alias: corInCluster, corInCluster,cogena-method, corInCluster,cogena_methods
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enrichment
(Package: cogena) :
get the enrichment table from a cogena object.
get the enrichment table from a cogena object with certain clustering methods and number of clusters.
● Data Source:
BioConductor
● Keywords:
● Alias: enrichment, enrichment,cogena-method, enrichment,cogena_methods
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gene2set
(Package: cogena) :
generate relationship between genes and gene-sets
Generate relationship between genes (gene SYMBOL) and gene-sets, such as Pathway or GO.
● Data Source:
BioConductor
● Keywords:
● Alias: annotationListToMatrix, gene2set
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