A modiefed parallel version of code imported from https://github.com/Bioconductor-mirror/ConsensusClusterPlus 1.11.1. Taken out of findModules.consensusCluster.R
Usage
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
)Arguments
- 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")