corInCluster {cogena} | R Documentation |
Correlation in the cluster of a cogena object. This is helpful if the number of genes in cluster are small.
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", ... )
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
|
type |
"full" (default), "upper" or "lower", display full
matrix, lower triangular or upper triangular matrix. See examples in
|
... |
other parameters to |
a correlation figure.
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)