View source: R/run.consensus.clustering.R
run.consensus.cluster | R Documentation |
A modiefed parallel version of code imported from https://github.com/Bioconductor-mirror/ConsensusClusterPlus 1.11.1. Taken out of findModules.consensusCluster.R
run.consensus.cluster( d, kGrid = NULL, repCount = NULL, diss = inherits(d, "dist"), pItem = NULL, pFeature = NULL, innerLinkage = NULL, distance = NULL, clusterAlg = NULL, weightsItem = NULL, weightsFeature = NULL, verbose = NULL, corUse = NULL )
d |
Required. A matrix where columns=items/samples and rows are features. For example, a gene expression matrix of genes in rows and microarrays in columns. OR ExpressionSet object. (Default = NULL) |
kGrid |
Optional. (Default = NULL) |
repCount |
Optional. Replicate count. (Default = NULL) |
diss |
Optional. A distance matrix of d. (Default = inherits( d, "dist" )) |
pItem |
Optional. A numerical value. proportion of items to sample. (Default = 0.8) |
pFeature |
Optional. A numerical value. proportion of features to sample. (Default = 1) |
innerLinkage |
Optional. A heirarchical linkage method for subsampling. (Default = "average") |
distance |
Optional. A character value. sample distance measures: "pearson","spearman", or "euclidean". (Default = "pearson") |
clusterAlg |
Optional. A character value. cluster algorithm. "hc" heirarchical (hclust) or "km" for kmeans. (Default = "kmeans") |
weightsItem |
Optional. A numerical vector. weights to be used for sampling items. (Default = NULL) |
weightsFeature |
Optional. AN umerical vector. weights to be used for sampling features. (Default = NULL) |
verbose |
Optional. A boolean when set to TRUE, prints messages to the screen to indicate progress. This is useful for large datasets.(Default = FALSE) |
corUse |
Optional. Use all cores avaiable. (Default = "Everything") |
Clustered consensus matrix. areaUnderCDF = areaK, consensus.matrix = cns.mtrx
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