corInCluster: Correlation in the cluster of a cogena object

In cogena: co-expressed gene-set enrichment analysis

Description

Correlation in the cluster of a cogena object. This is helpful if the number of genes in cluster are small.

Usage

corInCluster(
  object,
  method,
  nCluster,
  ith,
  corMethod = "pearson",
  plotMethod = "circle",
  type = "upper",
  ...
)

## S4 method for signature 'cogena'
corInCluster(
  object,
  method = clusterMethods(object),
  nCluster = nClusters(object),
  ith,
  corMethod = "pearson",
  plotMethod = "circle",
  type = "upper",
  ...
)

Arguments

object	a cogena object
method	a clustering method
nCluster	cluster number
ith	the i-th cluster (should no more than nCluster)
corMethod	a character string indicating which correlation coefficient (or covariance) is to be computed. One of "pearson" (default), "kendall", or "spearman", can be abbreviated.
plotMethod	the visualization method of correlation matrix to be used. Currently, it supports seven methods, named "circle" (default), "square", "ellipse", "number", "pie", "shade" and "color". See examples in corrplot for details
type	"full" (default), "upper" or "lower", display full matrix, lower triangular or upper triangular matrix. See examples in corrplot for details
...	other parameters to corrplot function.

Value

a correlation figure.

See Also

clEnrich corrplot

Examples

data(Psoriasis)
annofile <- system.file("extdata", "c2.cp.kegg.v7.01.symbols.gmt.xz", 
package="cogena")

## Not run: 
genecl_result <- coExp(DEexprs, nClust=2:3, clMethods=c("hierarchical","kmeans"), 
    metric="correlation", method="complete", ncore=2, verbose=TRUE)

clen_res <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)

corInCluster(clen_res, "kmeans", "3", "3")
corInCluster(clen_res, "kmeans", "3", "3", plotMethod="square")

## End(Not run)

cogena documentation built on Nov. 8, 2020, 6:54 p.m.