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.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)

[Package cogena version 1.26.0 Index]