Man pages for naglemi/mtmcskat
Multi-Threaded Monte Carlo Sequence Kernel Association Test (MTMC-SKAT)
| benchmark_nm | Benchmark the amount of RAM needed per permutation in a null... |
| calculate_max_perm_per_core | Calculate the number of permutations in a null model that can... |
| calculate_SKAT_empirical_p | Produce permuted p-values or empirical p-value for SKAT |
| chunk_windows | Divide a list of SNP windows into a chunk for each thread |
| determine_n_permutations | Estimate, based on initial p-values, the number of permut |
| determine_subset_pval_boundaries | Determine boundaries for subsetting SNP windows based on... |
| extract_window | Extract and format a window of SNPs to be tested in a SKAT... |
| mappable_SKAT | Obtain SKAT results, including permuted or empirical... |
| mtmcskat_NullModels | Run multi-threaded Monte Carlo Sequence Kernel Association... |
| MTMCSKAT_workflow | Run an automated MTMC-SKAT job |
| MTMCSKAT_workflow_pre_allocate_only | Run an automated MTMC-SKAT job |
| mtskat | Wrapper for SKAT sans resampling, with multi-threading over... |
| p_empirical_from_tally | Tally p-values from permuted null model to enable calculation... |
| pre_allocate | Pre-allocate a list of overlapping SNP windows |
| re_allocate_windows | Obtain a new list of SNP windows, based on p-values from an... |
| sample_mtmcskatnm1_results | MTMCSKAT results from multithreading over null models in a... |
| sample_mtmcskatnm2_results | MTMCSKAT results from multithreading over null models in two... |
| sample_mtmcskat_results | MTMCSKAT results from multithreading over SNP windows |
| sample_p_null_tallies | Tallies of p-values from resampling |
| sample_re_allocated_SNP_windows | List of selected SNP windows significantly associated with... |
| sample_SNP_window | Labeled window of alt. allele counts for P trichocarpa |
| sample_SNP_window_processed | Labeled window of alt. allele counts (filtered and imputed)... |
| sample_window_list | List of SNP window centers |
| select_windows_range_p | Select windows corresponding to p-values within range of... |
| SKAT_one_window | Run SKAT, optionally obtaining permuted p-values or empirical... |
| small_covariates | Covariates for poplar samples in stem regeneration experiment |
| small_mtskat_results | MTSKAT results from multithreading over SNP windows |
| small_phenodata | Proportions of poplar image pixels labeled as shoot |
| small_pre_allocated_windows | List of consecutive SNP windows with positon labels |
| small_pre_allocated_windows_processed | List of consecutive SNP windows (filtered and imputed) with... |
| subset_list_of_lists | Subset a list of lists to a list of desired lists only Subset... |
| tally_p_null | Multithreaded calculation of null p-values to enable... |
