Package: cophescan 1.4.1
Ichcha Manipur
cophescan: Adaptation of the Coloc Method for PheWAS
A Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see Manipur et al (2023) <doi:10.1101/2023.06.29.546856>.
Authors:
cophescan_1.4.1.tar.gz
cophescan_1.4.1.tar.gz(r-4.5-noble)cophescan_1.4.1.tar.gz(r-4.4-noble)
cophescan_1.4.1.tgz(r-4.4-emscripten)cophescan_1.4.1.tgz(r-4.3-emscripten)
cophescan.pdf |cophescan.html✨
cophescan/json (API)
NEWS
# Install 'cophescan' in R: |
install.packages('cophescan', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ichcha-m/cophescan/issues
- cophe_multi_trait_data - Simulated multi-trait data
Last updated 6 months agofrom:27ba87448d. Checks:OK: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 09 2024 |
R-4.5-linux-x86_64 | NOTE | Dec 09 2024 |
Exports:adjust_priorsaverage_piksaverage_piks_listaverage_posterior_probaverage_posterior_prob_listcombine.bfcophe_heatmapcophe_plotcophe.bf_bfcophe.hyp.predictcophe.multitraitcophe.prepare.dat.singlecophe.prepare.dat.susiecophe.singlecophe.single.lbfcophe.susiecophe.susie.lbfget_betaget_posterior_probHc.cutoff.fdrhypothesis.priorslogd_alphalogd_betalogd_gammalogliklogpostlogpriorslogsumlogsumexpmetrop_runmultitrait.simplifypars_initpars2pikper.snp.priorspiksplot_trait_manhatposterior_probprepare_plot_dataproposerun_metrop_priorssample_alphasample_betasample_gammasummary.cophetarget
Dependencies:clicoloccolorspacecrayondata.tabledplyrfansifarvergenericsggplot2ggrepelgluegridExtragtableirlbaisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmixsqpmunsellnlmepheatmappillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshaperlangscalessusieRtibbletidyselectutf8vctrsviridisviridisLitewithr
CoPheScan: Example with Fixed Priors
Rendered fromFixedPriors_03.Rmd
usingknitr::rmarkdown
on Dec 09 2024.Last update: 2024-03-12
Started: 2023-10-25
CoPheScan: Example with Hierarchical Priors
Rendered fromHierarchicalPriors_04.Rmd
usingknitr::rmarkdown
on Dec 09 2024.Last update: 2024-03-12
Started: 2023-10-25
CoPheScan: Input data
Rendered fromInputData_02.Rmd
usingknitr::rmarkdown
on Dec 09 2024.Last update: 2023-10-25
Started: 2023-10-25
Introduction to CoPheScan
Rendered fromIntroductionCoPheScan_01.Rmd
usingknitr::rmarkdown
on Dec 09 2024.Last update: 2023-10-25
Started: 2023-10-25