corInCluster {cogena}R Documentation

Correlation in the cluster of a cogena object

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.v5.0.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)
[Package cogena version 1.16.0 Index]