HIV_data: HIV Drug Resistance Database
In MTPS: Multi-Task Prediction using Stacking Algorithms
HIV R Documentation
HIV Drug Resistance Database
Description
The data from HIV Drug Resistance Database used for demonstration. After processing, YY contains 5 response variables variable for 1246 observations and XX are 228 predictors of those 1246 obsevations.
Format
Data objects used for demonstration
Details
In the HIV database, the resistance of five Nucleoside RT Inhibitor (NRTI) drugs were used as multivariate outcomes, including Lamivudine (3TC), Abacavir(ABC), Zidovudine (AZT), Stavudine (D4T), Didanosine (DDI). The mutation variables are used as the predictors. Some mutation variables were removed as they do not contain enough variation. The final outcome data is a matrix of size 1246 × 5, and the predictor data is a matrix of 1246 × 228 values, which is provided in the package called "HIV". In the example data in the package, "YY" refers the outcome data and "XX" refers the predictor data.
References
Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW. Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proceedings of the National Academy of Sciences. 2006 Nov 14;103(46):17355-60.
Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW. (2010). HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrobial Agents and Chemotherapy, 2010 Oct
Melikian GL, Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia-Cancio PV, Zolopa A, Robbins GK, Kagan R, Israelski D, Shafer RW (2012). Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility. Antimicrobial Agents and Chemother. 2012 May;56(5):2305-13.
Melikian GL, Rhee SY, Varghese V, Porter D, White K, Taylor J, Towner W, Troia P, Burack J, Dejesus E, Robbins GK, Razzeca K, Kagan R, Liu TF, Fessel WJ, Israelski D, Shafer RW (2013). Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. J Antimicrob Chemother, 2013 Aug 9.
Examples
data(HIV)
MTPS documentation built on July 9, 2023, 7:46 p.m.
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| HIV | R Documentation |
HIV Drug Resistance Database
Description
The data from HIV Drug Resistance Database used for demonstration. After processing, YY contains 5 response variables variable for 1246 observations and XX are 228 predictors of those 1246 obsevations.
Format
Data objects used for demonstration
Details
In the HIV database, the resistance of five Nucleoside RT Inhibitor (NRTI) drugs were used as multivariate outcomes, including Lamivudine (3TC), Abacavir(ABC), Zidovudine (AZT), Stavudine (D4T), Didanosine (DDI). The mutation variables are used as the predictors. Some mutation variables were removed as they do not contain enough variation. The final outcome data is a matrix of size 1246 × 5, and the predictor data is a matrix of 1246 × 228 values, which is provided in the package called "HIV". In the example data in the package, "YY" refers the outcome data and "XX" refers the predictor data.
References
Rhee SY, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, Shafer RW. Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proceedings of the National Academy of Sciences. 2006 Nov 14;103(46):17355-60.
Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW. (2010). HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrobial Agents and Chemotherapy, 2010 Oct
Melikian GL, Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia-Cancio PV, Zolopa A, Robbins GK, Kagan R, Israelski D, Shafer RW (2012). Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility. Antimicrobial Agents and Chemother. 2012 May;56(5):2305-13.
Melikian GL, Rhee SY, Varghese V, Porter D, White K, Taylor J, Towner W, Troia P, Burack J, Dejesus E, Robbins GK, Razzeca K, Kagan R, Liu TF, Fessel WJ, Israelski D, Shafer RW (2013). Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. J Antimicrob Chemother, 2013 Aug 9.
Examples
data(HIV)
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