co-expressed gene-set enrichment analysis


[Up] [Top]

Documentation for package ‘cogena’ version 1.0.0

Help Pages

annotationListToMatrix generate relationship between genes and gene-sets
clusterMethods Basic methods for a cogena object.
clusterMethods,cogena_methods Basic methods for a cogena object.
clusterMethods-method Basic methods for a cogena object.
clusters Basic methods for a cogena object.
clusters,cogena_methods Basic methods for a cogena object.
clusters-method Basic methods for a cogena object.
cogena co-expressed gene-set enrichment analysis
cogena-class An S4 class to represent co-expressed gene-set enrichment analysis result.
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
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 Get gene names in a certain cluster.
geneInCluster-method Get gene names in a certain cluster.
gmt2list read gmt file as a list
heatmapCluster heatmap of gene expression profilings with cluster indication.
heatmapCluster-method heatmap of gene expression profilings with cluster indication.
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.
heatmapPEI2 heatmap of the gene set enrichment_score matrix directly
heatmapPEI2,cogena heatmap of the gene set enrichment_score matrix directly
heatmapPEI2-method heatmap of the gene set enrichment_score matrix directly
hubgeneInCluster Show hub gene names in certain cluster.
hubgeneInCluster-method Show hub gene names in certain cluster.
mat Basic methods for a cogena object.
mat,cogena_methods Basic methods for a cogena object.
mat-method Basic methods for a cogena object.
nClusters Basic methods for a cogena object.
nClusters,cogena_methods Basic methods for a cogena object.
nClusters-method Basic methods for a cogena object.
optCluster get the best clustering methods and the number of clusters
optCluster,cogena get the best clustering methods and the number of clusters
optCluster-method get the best clustering methods and the number of clusters
PD Parkinson's Disease dataset.
PD,DEexprs,sampleLabel,cogena_result Parkinson's Disease dataset.
plot.sota Self-organizing tree algorithm (SOTA)
print.sota Self-organizing tree algorithm (SOTA)
sampleLabel label of samples
sota Self-organizing tree algorithm (SOTA)
summary-method Basic methods for a cogena object.