WorkflowEval: Workflow Option Evaluation

#############################################################################
  
  # TCGA-Assembler : An open-source R program for downloading, processing and analyzing public TCGA data.
  # Copyright (C) <2014>  <Yitan Zhu>
  # This file is part of TCGA-Assembler.

  #  TCGA-Assembler is free software: you can redistribute it and/or modify
  #  it under the terms of the GNU General Public License as published by
  #  the Free Software Foundation, either version 3 of the License, or
  #  (at your option) any later version.

  #  TCGA-Assembler is distributed in the hope that it will be useful,
  #  but WITHOUT ANY WARRANTY; without even the implied warranty of
  #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  #  GNU General Public License for more details.

  #  You should have received a copy of the GNU General Public License
  #  along with TCGA-Assembler.  If not, see <http://www.gnu.org/licenses/>.
  ############################################################################  


#####################################  Part I: Acquire Data  #########################################

# Clear workspace
#rm(list = ls());

# Load module A functions.
source("Module_A.r");

# Download level-3 miRNA-seq data of six rectum adenocarcinoma (READ) samples
# Rectum adenocarcinoma (READ): malignant tumor originating in rectum glandular epithelium
#miRNASeqRawData = DownloadmiRNASeqData(traverseResultFile = "./DirectoryTraverseResult_Jul-08-2014.rda", 
#  saveFolderName = "./QuickStartGuide_Results/RawData/", cancerType = "READ", 
#  assayPlatform = "miRNASeq", inputPatientIDs = c("TCGA-EI-6884-01", 
#  "TCGA-DC-5869-01", "TCGA-G5-6572-01", "TCGA-F5-6812-01", "TCGA-AF-2689-11", "TCGA-AF-2691-11")); 

# Download level-3 DNA copy number data of six READ samples
#CNARawData = DownloadCNAData(traverseResultFile = "./DirectoryTraverseResult_Jul-08-2014.rda", 
#  saveFolderName = "./QuickStartGuide_Results/RawData/", cancerType = "READ", 
#  assayPlatform = "genome_wide_snp_6", inputPatientIDs = c("TCGA-EI-6884-01",
#  "TCGA-DC-5869-01", "TCGA-G5-6572-01", "TCGA-F5-6812-01", "TCGA-AF-2692-10", "TCGA-AG-4021-10")); 

# Download level-3 RNASeqV2 gene expression and exon expression data of six READ samples
RNASeqRawData.V2 = DownloadRNASeqData(traverseResultFile = "./DirectoryTraverseResult_Jul-08-2014.rda", saveFolderName = 
  "./QuickStartGuide_Results/RawData/", cancerType = "READ", assayPlatform = "RNASeqV2", 
  dataType = "rsem.genes.normalized_results", inputPatientIDs = NULL);

RNASeqRawData.V1 = DownloadRNASeqData(traverseResultFile = "./DirectoryTraverseResult_Jul-08-2014.rda", saveFolderName = 
                                     "./QuickStartGuide_Results/RawData/", cancerType = "READ", assayPlatform = "RNASeqV1", 
                                   dataType = "gene.quantification", inputPatientIDs = NULL);

# Download level-3 HumanMethylation27 data of six READ samples
#Methylation27RawData = DownloadMethylationData(traverseResultFile = "./DirectoryTraverseResult_Jul-08-2014.rda", saveFolderName = 
#  "./QuickStartGuide_Results/RawData/", cancerType = "READ", assayPlatform = "humanmethylation27", 
#  inputPatientIDs = c("TCGA-AG-3583-01", "TCGA-AG-A032-01", "TCGA-AF-2692-11", "TCGA-AG-4001-01", 
#  "TCGA-AG-3608-01", "TCGA-AG-3574-01")); 

# Download level-3 HumanMethylation450 data of six READ samples
#Methylation450RawData = DownloadMethylationData(traverseResultFile = "./DirectoryTraverseResult_Jul-08-2014.rda", saveFolderName = 
#  "./QuickStartGuide_Results/RawData", cancerType = "READ", assayPlatform = "humanmethylation450", 
#  inputPatientIDs = c("TCGA-EI-6884-01", "TCGA-DC-5869-01", "TCGA-G5-6572-01", "TCGA-F5-6812-01", 
#  "TCGA-AG-A01W-11", "TCGA-AG-3731-11")); 

# Download level-3 RPPA protein expression data of six READ samples
RPPARawData = DownloadRPPAData(traverseResultFile = "./DirectoryTraverseResult_Jul-08-2014.rda", saveFolderName = 
  "./QuickStartGuide_Results/RawData", cancerType = "READ", assayPlatform = "mda_rppa_core", 
  inputPatientIDs = NULL);  

# Download de-identified clinical information of READ patients
DownloadClinicalData(traverseResultFile = "./DirectoryTraverseResult_Jul-08-2014.rda", saveFolderName = 
  "./QuickStartGuide_Results/RawData", cancerType = "READ", clinicalDataType = c("patient", "drug", "follow_up"));



#####################################  Part II: Basic Data Processing  #########################################

# Clear workspace
#rm(list = ls());

# Load module B functions.
source("Module_B.r");

# Process level-3 miRNA-seq data acquired by module A. 
#miRNASeqData = ProcessmiRNASeqData(inputFilePath = 
#  "./QuickStartGuide_Results/RawData/READ__bcgsc.ca__illuminahiseq_mirnaseq__GRCh37__Jul-08-2014.txt", 
#  outputFileName = "READ__illuminahiseq_mirnaseq", outputFileFolder = 
#  "./QuickStartGuide_Results/BasicProcessingResult");

# Process copy number data acquired by module A.
#READ.GeneLevel.CNA = ProcessCNAData(inputFilePath = 
#  "./QuickStartGuide_Results/RawData/READ__broad.mit.edu__genome_wide_snp_6__hg19__Jul-08-2014.txt", 
#  outputFileName = "READ__genome_wide_snp_6__GeneLevelCNA", outputFileFolder = 
#  "./QuickStartGuide_Results/BasicProcessingResult", refGenomeFile = "./SupportingFiles/Hg19GenePosition.txt");

#READ__unc.edu__illuminaga_rnaseq__gene.quantification__Jul-08-2014

# Process level-3 RNA-seq normalized gene expression data acquired by module A.
GeneExpData.V2 = ProcessRNASeqData(inputFilePath = 
  "./QuickStartGuide_Results/RawData/READ__unc.edu__illuminahiseq_rnaseqv2__rsem.genes.normalized_results__Jul-08-2014.txt", 
  outputFileName = "READ__illuminahiseq_rnaseqv2__GeneExp", outputFileFolder = 
  "./QuickStartGuide_Results/BasicProcessingResult", dataType = "GeneExp", verType = "RNASeqV2");

GeneExpData.V1 = ProcessRNASeqData(inputFilePath = 
                                  "./QuickStartGuide_Results/RawData/READ__unc.edu__illuminaga_rnaseq__gene.quantification__Jul-08-2014.txt", 
                                outputFileName = "READ__unc.edu__illuminaga_rnaseq__GeneExp", outputFileFolder = 
                                  "./QuickStartGuide_Results/BasicProcessingResult", dataType = "GeneExp", verType = "RNASeqV1");


# Process level-3 RNA-seq exon expression data acquired by module A.
#ExonExpData = ProcessRNASeqData(inputFilePath = 
#  "./QuickStartGuide_Results/RawData/READ__unc.edu__illuminahiseq_rnaseqv2__exon_quantification__Jul-08-2014.txt", 
#  outputFileName = "READ__illuminahiseq_rnaseqv2__ExonExp", outputFileFolder = 
#  "./QuickStartGuide_Results/BasicProcessingResult", dataType = "ExonExp", verType = "RNASeqV2");

# Process level-3 HumanMethylation27 data acquired by module A.
#Methylation27Data = ProcessMethylation27Data(inputFilePath = 
#  "./QuickStartGuide_Results/RawData/READ__jhu-usc.edu__humanmethylation27__Jul-08-2014.txt", 
#  outputFileName = "READ__humanmethylation27", outputFileFolder = "./QuickStartGuide_Results/BasicProcessingResult");

# Process level-3 HumanMethylation450 data acquired by module A.
#Methylation450Data = ProcessMethylation450Data(inputFilePath = 
#  "./QuickStartGuide_Results/RawData/READ__jhu-usc.edu__humanmethylation450__Jul-08-2014.txt", 
#  outputFileName = "READ__humanmethylation450", outputFileFolder = "./QuickStartGuide_Results/BasicProcessingResult");

# Process level-3 RPPA protein expression data acquired by module A.
RPPAData = ProcessRPPADataWithGeneAnnotation(
  inputFilePath = "./QuickStartGuide_Results/RawData/READ__mdanderson.org__mda_rppa_core__Jul-08-2014.txt", 
  outputFileName = "READ__mda_rppa_core", outputFileFolder = "./QuickStartGuide_Results/BasicProcessingResult");



#####################################  Part III: Advanced Data Processing  #########################################

# Clear workspace
#rm(list = ls());

# Load module B functions.
source("Module_B.r");

# Load READ methylation27 and methylation450 data.
#load("./QuickStartGuide_Results/BasicProcessingResult/READ__humanmethylation27.rda");
#Methylation27Data = list(Des = Des, Data = Data);
#load("./QuickStartGuide_Results/BasicProcessingResult/READ__humanmethylation450.rda");
#Methylation450Data = list(Des = Des, Data = Data);

# Merge READ methylation27 and methylation450 data.
#Methylation27_450_Merged = MergeMethylationData(input1 = Methylation27Data, input2 = 
#  Methylation450Data, outputFileName = "READ__humanmethylation27_450_merged", outputFileFolder = 
#  "./QuickStartGuide_Results/AdvancedProcessingResult");

# Calculate an average methylation value of CpG sites in each gene's region 
#Methylation450_OverallAverage = CalculateSingleValueMethylationData(input = Methylation450Data, 
#  regionOption = "All", DHSOption = "Both", outputFileName = "READ__humanmethylation450__SingleValue", 
#  outputFileFolder = "./QuickStartGuide_Results/AdvancedProcessingResult");

# Calculate an average methylation value of CpG sites within 1500 base pairs of 
# transcription start site (TSS) and hypersensitive to DNAse. 
#Methylation450_TSS1500_DHS = CalculateSingleValueMethylationData(input = Methylation450Data, 
#  regionOption = "TSS1500", DHSOption = "DHS", outputFileName = "READ__humanmethylation450__SingleValue", 
#  outputFileFolder = "./QuickStartGuide_Results/AdvancedProcessingResult");

# Extract methylation450 data of primary solid tumors.
#ExtractedData_TP = ExtractTissueSpecificSamples(inputData = Methylation450Data$Data, tissueType = "TP", 
#  singleSampleFlag = FALSE);

# Extract methylation450 data of primary solid tumors and solid normal tissues.
#ExtractedData_TP_NT = ExtractTissueSpecificSamples(inputData = Methylation450Data$Data, 
#  tissueType = c("TP", "NT"), singleSampleFlag = TRUE);

# Load multi-modal data of READ sampels
#load("./QuickStartGuide_Results/AdvancedProcessingResult/READ__humanmethylation450__SingleValue__All__Both.rda");
#READ__humanmethylation450__SingleValue__All__Both = list(Des = Des, Data = Data, dataType = "Methylation")
load("./QuickStartGuide_Results/BasicProcessingResult/READ__mda_rppa_core.rda");
READ__mda_rppa_core = list(Des = Des, Data = Data, dataType = "ProteinExp");
load("./QuickStartGuide_Results/BasicProcessingResult/READ__illuminahiseq_rnaseqv2__GeneExp.rda");
READ__illuminahiseq_rnaseqv2__GeneExp = list(Des = Des, Data = Data, dataType = "GeneExp");
load("./QuickStartGuide_Results/BasicProcessingResult/READ__unc.edu__illuminaga_rnaseq__GeneExp.rda");
READ__unc.edu__illuminaga_rnaseq__GeneExp = list(Des = Des, Data = Data, dataType = "GeneExp");

#READ__unc.edu__illuminaga_rnaseq__GeneExp.rda
#load("./QuickStartGuide_Results/BasicProcessingResult/READ__genome_wide_snp_6__GeneLevelCNA.rda");
#READ__genome_wide_snp_6__GeneLevelCNA = list(Des = Des, Data = Data, dataType = "CNA");
#load("./QuickStartGuide_Results/BasicProcessingResult/READ__illuminahiseq_mirnaseq__RPM.rda");
#READ__illuminahiseq_mirnaseq__RPM = list(Des = Des, Data = Data, dataType = "miRNAExp");

# Put multi-modal data in a vector of data list objects to be inputted into the data combination function.


inputDataList = vector("list", 2);
#inputDataList[[1]] = READ__illuminahiseq_rnaseqv2__GeneExp;
#inputDataList[[2]] = READ__humanmethylation450__SingleValue__All__Both;
inputDataList[[1]] = READ__unc.edu__illuminaga_rnaseq__GeneExp;
inputDataList[[2]] = READ__mda_rppa_core;
#inputDataList[[5]] = READ__illuminahiseq_mirnaseq__RPM;


# Merge multi-platform data
MergedData = CombineMultiPlatformData(inputDataList = inputDataList);

# Write the combined multi-platform data to into a tab-delimited txt file
write.table(cbind(MergedData$Des, MergedData$Data), 
  file = "./QuickStartGuide_Results/AdvancedProcessingResult/CombinedMultiPlatformDataV1.txt", 
  quote = FALSE, sep = "\t", na = "", col.names = TRUE, row.names = FALSE);