Man pages for agapow/subtypr
Robust and Validated Patient Subtyping for Precision Medicine

adjusted_rand_indexAdjusted rand index
analyze_survivalPlots the survival curves and compute the Cox p-value
breast_cancer_dataBreast cancer multi-omics data
check_distributionPlot the distribution of the features
consensus_spectral_clusteringApply consensus clustering on affinity matrix.
dunn_indexDunn index
entropyReturn entropy of vector
evaluationEvaluate parameters
flag_dataSimple quality control on sample-feature matrices
gbm_dataGlioblastoma multiforme (GBM) multi-omics data
generate_multi_moclustGenerate simulated data
generate_multi_structuredGenerate synthetic data based on a list of features matrics.
generate_multi_unstructuredGenerate a list of synthetic data matrices for validation
generate_partitionsGenerate a partitions matrix
generate_single_moclustGenerate simulated data
generate_synth_dataGenerate 'multi-omic' synthetic data matrices for validation
get_methodLoad built-in methods
get_metricLoad built-in metrics
helloHello, World!
homogeneity_completeness_vmeasureHomogeneity, completeness and V-Measure metrics for partition...
meila_viMeila's variation of information index
metrics_listMetrics implemented
mutual_informationCalculate mutual information of two vectors
normalized_mutual_informationNormalized mutual information
overview_metricsAn overview of the results with all available metrics
plot_affinity_matrixPlot clustered affinity matrix
plot_clinical_featuresBox-plot of clinical features for a given partition of the...
pre_processPre-process feature matrices before analysis.
select_featuresSelection of important features
select_madMean Absolute Deviation (MAD) cutoff
select_pcaApply principal components analysis
select_varianceVariance cutoff
silhouette_affinitySilhouette index for affinity matrix
silhouette_distanceClassic silhouette index for distance matrix
sparse_methylationSparse data to test tools
subtype_anfSubtypes using Affinity Network Fusion
subtype_pinsSubtypes using PINSPlus package
subtype_snfSubtypes patients using Similarity Network Fusion
tuningTunes the methods to have the best set of parameters
agapow/subtypr documentation built on Aug. 18, 2018, 10:37 p.m.