findModules.consensusCluster: Finds Consensus Clusters

In Sage-Bionetworks/metanetwork: Network meta analysis

Finds Consensus Clusters

Description

A modiefed parallel version of code imported from https://github.com/Bioconductor-mirror/ConsensusClusterPlus 1.11.1

Usage

findModules.consensusCluster(
  d = NULL,
  maxK = 100,
  reps = 100,
  pItem = 0.8,
  pFeature = 1,
  clusterAlg = "kmeans",
  innerLinkage = "average",
  distance = "pearson",
  changeCDFArea = 0.001,
  nbreaks = 20,
  seed = 123456789.12345,
  weightsItem = NULL,
  weightsFeature = NULL,
  corUse = "everything",
  verbose = F
)

Arguments

d	Optional. 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)
maxK	Optional. An integer value. maximum cluster number to evaluate. (Default = 100)
reps	Optional. An integer value. number of subsamples. (Default = 100)
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)
clusterAlg	Optional. A character value. cluster algorithm. "hc" heirarchical (hclust) or "km" for kmeans. (Default = "kmeans")
innerLinkage	Optional. A heirarchical linkage method for subsampling. (Default = "average")
distance	Optional. A character value. sample distance measures: "pearson","spearman", or "euclidean". (Default = "pearson")
changeCDFArea	Optional. Minimum spline distance for seq(2,'maxK', length.out = 'nbreaks') (Default = 0.001)
nbreaks	Optional. Number of breaks to use in seq(2,'maxK',length.out = 'nbreaks') this becomes the kGrid argument in run.consensus.cluster. (Default = 20)
seed	Optional, A numerical value. Sets random seed for reproducible results. (Default = 123456789.12345)
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)
corUse	Optional. Use all cores avaiable. (Default = "Everything")
verbose	Optional. A boolean when set to TRUE, prints messages to the screen to indicate progress. This is useful for large datasets.(Default = FALSE)

Value

Final clustered modules.

Sage-Bionetworks/metanetwork documentation built on April 27, 2022, 7:42 a.m.