# co-expressed gene-set enrichment analysis

## Documentation for package ‘cogena’ version 1.24.0

- 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.