Man pages for USCbiostats/hJAM
Hierarchical Joint Analysis of Marginal Summary Statistics
| EN.hJAM | Elastic net hJAM |
| ENhJAM.SimulationSet | Simulation data for EN-hJAM |
| get_XtX | Get transformed statistics: XtX |
| get_yty | Get transformed statistics: yty |
| get_z | Get transformed statistics: z, or Xty |
| GTEx.PrCa | Real data for selecting the genes on chromosome 10 for the... |
| hJAM | hJAM Fit hJAM with linear regression |
| hJAM_egger | hJAM_egger Fit hJAM with Egger regression |
| JAM_A | Compute conditional A matrix |
| JAM_alphas | Compute conditional alphas |
| LogisticToLinearEffects | Transform log odds ratios to linear effects |
| MI | Example data of hJAM |
| mJAM_build_CS | Construct mJAM credible set based for selected index SNP |
| mJAM_Forward | Run mJAM with Forward Selection |
| mJAM_get_condp | Get conditional p-value under mJAM model |
| mJAM_get_condp_selected | Get conditional p-value for selected (index SNPs) under mJAM... |
| mJAM_get_PrM | Get Pr(Model) based on BF-type model probability |
| mJAM_get_PrMed | Get Pr(Mediation) based on causal mediation models |
| mJAM_get_PrM_Wald | Get Pr(Model) based on Wald-type model probability |
| mJAM_LDpruning | Pruning SNPs based on LD |
| mJAM_SuSiE | Run mJAM with SuSiE |
| mJAM_SuSiE_get_cs | Get and tidy SuSiE credible sets |
| output.format | Keep the output as three digits |
| PrCa.lipids | Real data for selecting the metabolites for the risk of... |
| print.ENhJAM | Print out for EN-hJAM |
| print.hJAM | Print out for hJAM |
| print.hJAM_egger | Print out for hJAM_egger |
| print.SHAJAM | Print out for SHA-JAM |
| SHAJAM | SHA-JAM Fit SHA-JAM |
| SNPs_heatmap | Heatmap for all the SNPs used in the analysis |
| SNPs_scatter_plot | Scatter plot for SNPs vs. one intermediate in the analysis |
| susie_get_posterior_mean_v2 | Get SuSiE posterior mean |
| susie_get_posterior_sd_v2 | Get SuSiE posterior sd |
| susieJAM_A | Compute conditional A using SuSiE JAM |
| susieJAM_alphas | Compute conditional alphas using SuSiE JAM |
