Package: PRSPGx 0.3.0
PRSPGx: Construct PGx PRS
Construct pharmacogenomics (PGx) polygenic risk score (PRS) with PRS-PGx-Unadj (unadjusted), PRS-PGx-CT (clumping and thresholding), PRS-PGx-L, -GL, -SGL (penalized regression), PRS-PGx-Bayes (Bayesian regression). Package is based on ''Pharmacogenomics Polyenic Risk Score for Drug Response Prediction Using PRS-PGx Methods'' by Zhai, S., Zhang, H., Mehrotra, D.V., and Shen, J., 2021 (submitted).
Authors:
PRSPGx_0.3.0.tar.gz
PRSPGx_0.3.0.zip(r-4.5)PRSPGx_0.3.0.zip(r-4.4)PRSPGx_0.3.0.zip(r-4.3)
PRSPGx_0.3.0.tgz(r-4.4-any)PRSPGx_0.3.0.tgz(r-4.3-any)
PRSPGx_0.3.0.tar.gz(r-4.5-noble)PRSPGx_0.3.0.tar.gz(r-4.4-noble)
PRSPGx_0.3.0.tgz(r-4.4-emscripten)PRSPGx_0.3.0.tgz(r-4.3-emscripten)
PRSPGx.pdf |PRSPGx.html✨
PRSPGx/json (API)
| # Install 'PRSPGx' in R: |
| install.packages('PRSPGx', repos = c('https://zsviolet.r-universe.dev', 'https://cloud.r-project.org')) |
- PRSPGx.example - Simulated example data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:6e2011e644. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 01 2024 |
| R-4.5-win | OK | Sep 01 2024 |
| R-4.5-linux | OK | Sep 01 2024 |
| R-4.4-win | OK | Sep 01 2024 |
| R-4.4-mac | OK | Sep 01 2024 |
| R-4.3-win | OK | Sep 01 2024 |
| R-4.3-mac | OK | Sep 01 2024 |
Exports:PRS_Dis_CTPRS_Dis_LDpred2PRS_PGx_BayesPRS_PGx_CTPRS_PGx_Lasso
Dependencies:bdsmatrixBHbigassertrbigparallelrbigreadrbigsnprbigsparserbigstatsrbigutilsrbitclicodacodetoolscolorspacecowplotdata.tableDEoptimRdigestdoParalleldoRNGfansifarverffflockforeachgglassoggplot2GIGrvgglmnetgluegmmgtableisobanditeratorslabelinglatticelifecyclelmtestmagrittrMASSMatrixmatrixcalcMatrixModelsmcmcMCMCpackmgcvminpack.lmmunsellmvtnormnabornlmeparallellypillarpkgconfigpropagatepsquantregR6RColorBrewerRcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratRfastRhpcBLASctlrlangrmiorngtoolsrobustbaseroptimRSpectrarunoncesandwichscalesSGLshapeSparseMsurvivaltibbletmvtnormtriebeardurltoolsutf8vctrsviridisLitewithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Construct disease PRS unadjusted or using clumping and thresholding | PRS_Dis_CT |
| Construct disease PRS using LDpred2 | PRS_Dis_LDpred2 |
| Construct PGx PRS using Bayesian regression | PRS_PGx_Bayes |
| Construct PGx PRS unadjusted or using clumping and thresholding | PRS_PGx_CT |
| Construct PGx PRS using penalized regression | PRS_PGx_Lasso |
| Simulated example data | PRSPGx.example |
