co-expressed gene-set enrichment analysis

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Documentation for package ‘cogena’ version 1.42.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

AllGeneSymbols	All the gene symbols
annotationListToMatrix	generate relationship between genes and gene-sets
clEnrich	Gene set enrichment for clusters
clEnrich_one	Gene set enrichment for clusters (for one clustering method and a certain number of clusters)
clusterMethods	Basic methods for a genecl object.
clusterMethods,cogena_methods	Basic methods for a genecl object.
clusterMethods,genecl_methods	Basic methods for a genecl object.
clusterMethods-method	Basic methods for a genecl object.
coExp	co-expressed gene-set enrichment analysis
cogean_package	Co-expressed gene set enrichment analysis
cogena	Co-expressed gene set enrichment analysis
cogena-class	An S4 class to represent co-expressed gene-set enrichment analysis result.
cogena_package	Co-expressed gene set enrichment analysis
corInCluster	Correlation in the cluster of a cogena object
corInCluster,cogena_methods	Correlation in the cluster of a cogena object
corInCluster-method	Correlation in the cluster of a cogena object
DEexprs	gene expression of DEG
enrichment	get the enrichment table from a cogena object.
enrichment,cogena_methods	get the enrichment table from a cogena object.
enrichment-method	get the enrichment table from a cogena object.
gene2set	generate relationship between genes and gene-sets
genecl-class	An S4 class to represent co-expressed gene
geneclusters	geneclusters: get the cluster information of a certain clustering method with a certain number.
geneclusters,cogena_methods	geneclusters: get the cluster information of a certain clustering method with a certain number.
geneclusters,genecl_methods	geneclusters: get the cluster information of a certain clustering method with a certain number.
geneclusters-method	geneclusters: get the cluster information of a certain clustering method with a certain number.
geneExpInCluster	Get gene names in each clusters and the expression profiling.
geneExpInCluster,cogena_methods	Get gene names in each clusters and the expression profiling.
geneExpInCluster-method	Get gene names in each clusters and the expression profiling.
geneInCluster	Get gene names in a certain cluster.
geneInCluster,cogena_methods,cluster_methods	Get gene names in a certain cluster.
geneInCluster-method	Get gene names in a certain cluster.
gmt2list	read gmt file as a list
gmtlist2file	write gmt list into gmt file
heatmapCluster	heatmap of gene expression profilings with cluster indication.
heatmapCluster-method	heatmap of gene expression profilings with cluster indication.
heatmapCmap	heatmap designed for for CMap gene set only
heatmapCmap,cogena	heatmap designed for for CMap gene set only
heatmapCmap-method	heatmap designed for for CMap gene set only
heatmapPEI	heatmap of the gene set enrichment from a cogena object.
heatmapPEI,cogena	heatmap of the gene set enrichment from a cogena object.
heatmapPEI-method	heatmap of the gene set enrichment from a cogena object.
logfc	Show up or down-regualted genes for a clustering method and the number of clusters.
logfc,	Show up or down-regualted genes for a clustering method and the number of clusters.
mat	mat: get the original data from a genecl object.
mat,cogena_methods	mat: get the original data from a genecl object.
mat,genecl_methods	mat: get the original data from a genecl object.
mat-method	mat: get the original data from a genecl object.
nClusters	nClusters: get the number of clusters from a genecl object.
nClusters,cogena_methods	nClusters: get the number of clusters from a genecl object.
nClusters,genecl_methods	nClusters: get the number of clusters from a genecl object.
nClusters-method	nClusters: get the number of clusters from a genecl object.
PEI	Significance of Gene sets enrichment.
plot.sota	Self-organizing tree algorithm (SOTA)
print.sota	Self-organizing tree algorithm (SOTA)
Psoriasis	Psoriasis dataset.
Psoriasis,DEexprs,sampleLabel,cogena_result	Psoriasis dataset.
sampleLabel	label of samples
show,cogena_methods	show: show the class of cogena or genecl object
show-method	show: show the class of cogena or genecl object
sota	Self-organizing tree algorithm (SOTA)
summary,cogena_methods	summary: a summary of a genecl object.
summary-method	summary: a summary of a genecl object.
upDownGene	Show up or down-regualted genes for a clustering method and the number of clusters.
upDownGene,cogena	Show up or down-regualted genes for a clustering method and the number of clusters.
upDownGene-method	Show up or down-regualted genes for a clustering method and the number of clusters.