This script will create a drug sensitivity prediction for every sample in TCGA. Set the root directory to the location of the data. This must be modifed for your own use (based on the location of the files).
theRootDir <- "/mnt/data_scratch/finalData/"
dir.create(paste(theRootDir, "dataOut/", sep = ""), showWarnings = FALSE)
library(pRRophetic)
## Warning: replacing previous import by 'genefilter::Anova' when loading
## 'pRRophetic'
load(file=paste(theRootDir, "dataIn/tenRuvNewStandardApproach.RData", sep="")) # cancerTypesVec, tenRuvNewStandardApproach
diseaseAbbrvs <- c("ACC", "BLCA", "BRCA", "CESC", "CHOL", "COAD", "DLBC", "GBM", "HNSC", "KICH", "KIRC", "KIRP", "LAML", "LGG", "LIHC", "LUAD", "LUSC", "MESO", "OV", "PAAD", "PCPG", "PRAD", "READ", "SARC", "SKCM", "STAD", "TGCT", "THCA", "THYM", "UCEC", "UCS", "UVM")
possibleDrugs <- c("A.443654", "A.770041", "ABT.263", "ABT.888", "AG.014699", "AICAR", "AKT.inhibitor.VIII", "AMG.706", "AP.24534", "AS601245", "ATRA", "AUY922", "Axitinib", "AZ628", "AZD.0530", "AZD.2281", "AZD6244", "AZD6482", "AZD7762", "AZD8055", "BAY.61.3606", "Bexarotene", "BI.2536", "BIBW2992", "Bicalutamide", "BI.D1870", "BIRB.0796", "Bleomycin", "BMS.509744", "BMS.536924", "BMS.708163", "BMS.754807", "Bortezomib", "Bosutinib", "Bryostatin.1", "BX.795", "Camptothecin", "CCT007093", "CCT018159", "CEP.701", "CGP.082996", "CGP.60474", "CHIR.99021", "CI.1040", "Cisplatin", "CMK", "Cyclopamine", "Cytarabine", "Dasatinib", "DMOG", "Docetaxel", "Doxorubicin", "EHT.1864", "Elesclomol", "Embelin", "Epothilone.B", "Erlotinib", "Etoposide", "FH535", "FTI.277", "GDC.0449", "GDC0941", "Gefitinib", "Gemcitabine", "GNF.2", "GSK269962A", "GSK.650394", "GW.441756", "GW843682X", "Imatinib", "IPA.3", "JNJ.26854165", "JNK.9L", "JNK.Inhibitor.VIII", "JW.7.52.1", "KIN001.135", "KU.55933", "Lapatinib", "Lenalidomide", "LFM.A13", "Metformin", "Methotrexate", "MG.132", "Midostaurin", "Mitomycin.C", "MK.2206", "MS.275", "Nilotinib", "NSC.87877", "NU.7441", "Nutlin.3a", "NVP.BEZ235", "NVP.TAE684", "Obatoclax.Mesylate", "OSI.906", "PAC.1", "Paclitaxel", "Parthenolide", "Pazopanib", "PD.0325901", "PD.0332991", "PD.173074", "PF.02341066", "PF.4708671", "PF.562271", "PHA.665752", "PLX4720", "Pyrimethamine", "QS11", "Rapamycin", "RDEA119", "RO.3306", "Roscovitine", "Salubrinal", "SB.216763", "SB590885", "Shikonin", "SL.0101.1", "Sorafenib", "S.Trityl.L.cysteine", "Sunitinib", "Temsirolimus", "Thapsigargin", "Tipifarnib", "TW.37", "Vinblastine", "Vinorelbine", "Vorinostat", "VX.680", "VX.702", "WH.4.023", "WO2009093972", "WZ.1.84", "X17.AAG", "X681640", "XMD8.85", "Z.LLNle.CHO", "ZM.447439")
allDrugPredictions <- list()
for(i in 1:length(possibleDrugs))
{
allDrugPredictions[[i]] <- pRRopheticPredict(tenRuvNewStandardApproach, possibleDrugs[i], selection=1, batchCorrect="standardize", removeLowVaryingGenes=0.2, removeLowVaringGenesFrom="rawData")
}
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4399 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4397 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4397 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4402 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4402 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4402 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4433 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4382 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4402 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4433 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4399 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4399 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4433 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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## 11503 gene identifiers overlap between the supplied expression matrices...
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## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4402 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4381 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4404 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4380 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4383 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4397 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4382 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4404 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4398 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
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##
## 11503 gene identifiers overlap between the supplied expression matrices...
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##
## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
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## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4381 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4397 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4397 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4433 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4397 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4380 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4382 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4399 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4402 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4385 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4391 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4433 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4392 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4399 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4400 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4430 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4402 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4403 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4382 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4386 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
##
##
## 11503 gene identifiers overlap between the supplied expression matrices...
##
##
## 4401 low variabilty genes filtered.
## Fitting Ridge Regression model... Done
##
## Calculating predicted phenotype...Done
names(allDrugPredictions) <- possibleDrugs
allDrugPredictions_mat <- do.call(rbind, allDrugPredictions)
Save out the drug predictions on all of TCGA. These will be used in subsequent analysis…..
save(allDrugPredictions, file=paste(theRootDir, "dataOut/allDrugPredictions.RData", sep=""))
save(allDrugPredictions_mat, cancerTypesVec, file=paste(theRootDir, "dataOut/allDrugPredictions_mat.RData", sep=""))