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:Ichcha Manipur [aut, cre], Chris Wallace [aut]

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Bug tracker:https://github.com/ichcha-m/cophescan/issues

On CRAN:

45 exports 6 stars 1.75 score 46 dependencies 24 scripts 943 downloads

Last updated 3 months agofrom:fa0d323634. Checks:OK: 1 NOTE: 8. Indexed: yes.

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