Cancer subtypes identification, validation and visualization based on multiple genomic data sets

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Documentation for package ‘CancerSubtypes’ version 1.26.0

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affinityMatrix This is the affinity Matrix function extracted from SNFtool package. Computes affinity matrix from a generic distance matrix
data.checkDistribution Data check distribution
data.imputation Data imputation
data.normalization Data normalization
DiffExp.limma DiffExp.limma
dist2 This is the distance function extracted from SNFtool package. Computes the Euclidean distances between all pairs of data point given.
drawHeatmap Generate heatmaps
ExecuteCC Execute Consensus Clustering
ExecuteCNMF Execute Consensus NMF (Nonnegative matrix factorization)
ExecuteiCluster Execute iCluster (Integrative clustering of multiple genomic data)
ExecuteSNF Execute SNF(Similarity Network Fusion )
ExecuteSNF.CC Execute the combined SNF (Similarity Network Fusion) and Consensus clustering
ExecuteWSNF Execute the WSNF(Weighted Similarity Network Fusion)
FSbyCox Biological feature (such as gene) selection based on Cox regression model.
FSbyMAD Biological feature (such as gene) selection based on the most variant Median Absolute Deviation (MAD).
FSbyPCA Biological feature (such as gene) dimension reduction and extraction based on Principal Component Analysis.
FSbyVar Biological feature (such as gene) selection based on the most variance.
GeneExp Dataset: Gene expression
miRNAExp Dataset: miRNA expression
Ranking Dataset: A default ranking of features for the fuction ExecuteWSNF()
saveFigure This function save the figure in the current plot.
sigclustTest A statistical method for testing the significance of clustering results.
silhouette_SimilarityMatrix Compute or Extract Silhouette Information from Clustering based on similarity matrix.
spectralAlg This is an internal function but need to be exported for the function ExecuteSNF.CC() call.
status Dataset: Survival status
survAnalysis Survival analysis(Survival curves, Log-rank test) and compute Silhouette information for cancer subtypes
time Dataset: Survival time