Man pages for kjgleason/primo
Package in R for Integrative Multi-Omics association analysis
| append_Primo_obj | Append a Primo object. |
| calc_Dmatrix | Density matrix calculation |
| calc_fdr | Calculate the empirical false discovery rate (FDR). |
| calc_fdr_col | Calculate the empirical false discovery rate (FDR) for a... |
| calc_fdr_conditional | Calculate the empirical false discovery rate (FDR) after... |
| calc_fdr_multi | Calculate the empirical false discovery rate (FDR) for each... |
| chiMix_pDiff | Difference from nominal P-values of a chi-squared mixture. |
| collapse_pp_combin | Collapse posterior probabilities of association for... |
| collapse_pp_num | Collapse posterior probabilities based on number of traits of... |
| collapse_pp_trait | Collapse posterior probabilities of association for each... |
| em_iter | EM Iteration |
| e_step | E-step |
| e_step_withColSums | E-step, with column sums of posterior probabilities |
| estimate_densities | Estimate parameters under the null and alternative densities |
| estimate_densities_modT | Estimate parameters under the null and alternative densities |
| estimate_densities_pval | Estimate parameters under the alternative density |
| find_leadsnps | Find the lead SNP for each phenotype in each region. |
| make_qmat | Create association pattern matrix |
| m_step | M-step |
| Primo | Estimate posterior probabilities of association patterns. |
| Primo_chiMix | Estimate posterior probabilities of association patterns,... |
| Primo_conditional | Perform conditional analysis for a specified variant. |
| Primo_missdata_pval | Estimate posterior probabilities for observations missing... |
| Primo_missdata_tstat | Estimate posterior probabilities for observations missing... |
| Primo_modT | Estimate posterior probabilities of association patterns,... |
| primo-package | Primo: Package in R for Integrative Multi-Omics association... |
| Primo_pval | Estimate posterior probabilities of association patterns,... |
| Primo_tstat | Estimate posterior probabilities of association patterns,... |
| run_conditional | Set up conditional analysis for specified variant(s) by... |
| run_conditional_gwas | Conditional analysis for known complex trait-associated... |
| subset_Primo_obj | Subset a Primo object. |
