This file provides instruction for data analysis reported in the manuscript. If you encounters any error or anything is missing, please let me know. My email is tin@wayne.edu.

First, download PINS package PINS_1.0.tar.gz

Second, please download the following 8 mRNA datasets: 
AML2004.RData, Brain2002.RData, GSE10245.RData, GSE14924.RData, GSE15061.RData, GSE19188.RData, GSE43580.RData, Lung2001.RData

Third, download the TCGA data:
BRCA.zip, COAD.zip, GBM.zip, KIRC.zip, LAML.zip, LUSC.zip


Fourth, download the METABRIC datasets:
METABRIC_discovery.RData, METABRIC_validation.RData


Finally, download the scripts compressed in the file Scripts.zip


Below are the scripts used for the data analyses:

1/ CCClusteringGEO.R : Analysis of 8 mRNA datasets using Consensus Clustering (CC)
2/ CCClusteringMetabric.R : Analysis of METABRIC datasets using CC
3/ CCClusteringTCGA.R : Analysis of TCGA data using CC
4/ CCClusteringTCGA_2type.R : Analysis of TCGA data (2 data types) using CC


5/ iClusterPlusGEO.R : Analysis of 8 mRNA datasets using iClusterPlus
6/ iClusterPlusGEO_MoreDimensions.R : Analysis of 8 mRNA datasets (more dimensions) using iClusterPlus
7/ iClusterPlusMetabric.R : Analysis of METABRIC datasets using iClusterPlus
8/ iClusterPlusTCGA.R : Analysis of TCGA data using iClusterPlus
9/ iClusterPlusTCGA_2type.R : Analysis of TCGA data (2 data types) using iClusterPlus


10/ PINSClusteringGEO.R : Analysis of 8 mRNA datasets using PINS
11/ PINSClusteringMetabric.R : Analysis of METABRIC datasets using PINS
12/ PINSClusteringTCGA.R : Analysis of TCGA data using PINS
13/ PINSClusteringTCGA_2types.R : Analysis of TCGA data (2 types) using PINS
14/ PINSClusteringTCGA_MoreAnalysis.R : Analysis of TCGA data using PINS with many agreement cutoffs
15/ PINSSimulation.R : Simulation analysis using PINS
16/ PINSClusteringGEO_Stability.R : Analysis of mRNA datasets using PINS with different perturbation magnitude


17/ SNFClusteringGEO.R : Analysis of 8 mRNA datasets using SNF
18/ SNFClusteringGEO_MoreAnalysis.R : Analysis of mRNA datasets using SNF with different alpha values
19/ SNFClusteringMetabric.R : Analysis of METABRIC datasets using SNF
20/ SNFClusteringTCGA.R : Analysis of TCGA data using SNF
21/ SNFClusteringTCGA_2type.R : Analysis of TCGA data (2 types) using SNF

22/ SilhouetteTCGA.R : Analysis of TCGA data using maxSilhouette
23/ iClusterPlusTCGA_2type.R : Analysis of TCGA data (2 types) using maxSilhouette

24/ TCGASilhouetteAndCI.R : Calculate concordance index and silhouette scores for PINS, CC, SNF, iClusterPlus, and maxSilhouette
25/ PlotTCGAResults.R : Plot TCGA figures and calculate Cox p-values
26/ PlotSimulation.R : Plot simulation figures
27/ PlotMetabricResults.R : Plot METABRIC results
28/ PlotGEOResults.R : Plot results of 8 mRNA datasets, plus Rand Index and Adjusted Rand Index
29/ PINS_Mutations.R : Mutation analysis of PINS subtypes
30/ BasicFunctions.R : Basic functions in case the scripts need some functions
