Package: cause 1.2.0.0335

Jean Morrison

cause: CAUSE: Causal Analysis Using Summary Effect Estimates

Identify causal patterns using pairs of GWAS summary statistics.

Authors:Jean Morrison

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cause.pdf |cause.html✨
cause/json (API)

# Install 'cause' in R:
install.packages('cause', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jean997/cause/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

4.39 score 53 stars 93 scripts 30 exports 67 dependencies

Last updated 3 years agofrom:6257e6c66e. Checks:OK: 1 WARNING: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-win-x86_64WARNINGNov 23 2024
R-4.5-linux-x86_64WARNINGNov 23 2024
R-4.4-win-x86_64WARNINGNov 23 2024
R-4.4-mac-x86_64WARNINGNov 23 2024
R-4.4-mac-aarch64WARNINGNov 23 2024
R-4.3-win-x86_64WARNINGNov 23 2024
R-4.3-mac-x86_64WARNINGNov 23 2024
R-4.3-mac-aarch64WARNINGNov 23 2024

Exports:causecause_download_example_gwas_datacause_grid_adaptest_cause_paramsgwas_formatgwas_mergein_sample_elpd_loold_pruneloglikloglik_ijloglik_ij_Z0loglik_ij_Z1loglik_loologlik_matloglik_samps_Z0loglik_samps_Z1map_pi_rhomap_pi_rho_nonnull_eqgmap_pi_rho_nonnull_fixedmap_pi_rho_nonnull_geqmap_pi_rho_nonnull_qgenew_cause_datanew_cause_data_fitread_standard_formatrecompute_elpd_tablesamp_from_gridsetup_cause_pipelinesetup_gwas_pairsstep_quantilevariance_pair_candidates

Dependencies:abindashrbackportsbitbit64checkmateclicliprcolorspacecpp11crayondistributionaldplyretrunctfansifarvergenericsggplot2gluegridExtragtablehmsintervalsinvgammairlbaisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmixsqpmunsellnlmenumDerivpillarpkgconfigposteriorprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloRcppParallelreadrrlangscalesSQUAREMstringistringrtensorAtibbletidyrtidyselecttruncnormtzdbutf8vctrsviridisLitevroomwithr

Readme and manuals

Help Manual

Help pageTopics
Adaptive grid estimation of posteriorsadapt2_grid
CAUSEcause
Download GWAS data to use in examplescause_download_example_gwas_data
CAUSE posterior density estimationcause_grid_adapt
Estimate CAUSE Nuisance Parametersest_cause_params
Estimate CAUSE Nuisance Parametersest_cause_params_future
Prior variance for gamma and etaeta_gamma_prior
Convert GWAS summary statistics to a standard formatgwas_format
Format data for CAUSEgwas_merge
Estimate delta elpd for pairs of modelsin_sample_elpd_loo
Prune variants for LDld_prune
Calculate likelihood - version 7loglik
Calculate likelihood of (beta_hat_1[j], beta_hat_2[j])) given rho, b, sigma_1j, sigma_2j, s_1j, s_2j where alpha_kj ~ N(0, sigma_kj)loglik_ij
Calculate likelihood matrix for LOO (SNPs by posterior samples)loglik_loo
Calculate likelihood matrix - version 7loglik_mat
Calculate likelihood matrix for LOO (SNPs by posterior samples)loglik_samps_Z0
Calculate likelihood matrix for LOO (SNPs by posterior samples)loglik_samps_Z1
Estimate pi and mixture proportions under null modelmap_pi_rho
Estimate pi and mixture proportions under a specified modelmap_pi_rho_nonnull
Estimate pi and mixture proportions under a specified modelmap_pi_rho_nonnull_eqg
Estimate pi and mixture proportions under a specified modelmap_pi_rho_nonnull_fixed
Estimate pi and mixture proportions under a specified modelmap_pi_rho_nonnull_geq
Estimate pi and mixture proportions under a specified modelmap_pi_rho_nonnull_qge
Create a new cause_data objectnew_cause_data
Create a new cause_data_fit objectnew_cause_data_fit
Plot CAUSEplot.cause
Plot posteriors for one CAUSE fitplot.cause_post
Print CAUSE Summaryprint.cause_summary
Print CAUSE fit Summaryprint.summary_cause_post
Recompute elpd table for a CAUSE fit that is already computedrecompute_elpd_table
Sample from grid approximation of posterior distribuitionssamp_from_grid
Set up analysis directory for pairs of GWAS summary statisticssetup_cause_pipeline
Set up analysis directory for pairs of GWAS summary statisticssetup_gwas_pairs
Quantile of a step pdfstep_quantile
Summarize CAUSE Resultssummary.cause
Summarize CAUSE Results for a single fitsummary.cause_post
Posterior probability of acting through UZ_post