Man pages for FireGutter/geneference
Simulating and analysing genes with LT-FH
| analysis_association | Run association analysis |
| assign_GWAX_phenotype | Create phenotype status by proxy |
| assign_ltfh_phenotype | Calculate posterior mean genetic liabilities |
| augment_results | Augment results for plotting |
| calculate_cov | Calculate covariance matrix of liabilities |
| calculate_error_types | Calculate error types |
| compare_beta | Plot transformed linear GWAS beta values against the... |
| convert_geno_file | Convert files to .bed |
| covmatrix | Create covariance matrix for liabilities |
| create_map | Create .map-file for PLINK |
| data_for_testsim | Small dataset of simulated genotypes |
| load_phenotypes | Import phenotype data |
| load_results | Import and merge results |
| n_sibs | Find number of siblings in largest family |
| pipe | Pipe operator |
| plot_estimates_vs_true | Plot true effects against estimated effects of SNPs |
| plot_manhattan | Manhattan plot of p-values |
| plot_pmgl_vs_true | Plot true genetic liabilities against posterior mean genetic... |
| plot_pval_hist | Plot a histogram of p-values |
| plot_pval_QQ | Plot a QQ-plot of p-values |
| rmnorm | Multivariate normal distributions |
| sim_fixed_family | Simulation with fixed family size |
| sim_no_family | Simulation without family history |
| sim_random_family | Simulation with random family sizes |
| sim_test | Simulation directly in the R session without family history |
| sim_varied_family | Simulation with varying family sizes |
| to_ped | Format conversion |
