| add_ref_annotations | 'add_ref_annotations' integrate GWAS summary data with... |
| align_alleles | 'align_alleles' compute variance weighted euclidean distance... |
| ambiguous | 'ambiguous' get ambiguous variants |
| basis.trait.proj | Burren sparse basis files |
| beta.centers | Burren sparse basis files |
| comp | 'comp' get complement for a set of variants |
| compute_seb_proj_var | analytically compute the variance of a projection given a... |
| compute_seb_proj_var_sparse | analytically compute the variance of a projection given a... |
| compute_shrinkage_metrics | This function computes various shrinkage metrics... |
| control_prior_shape | This function computes shape parameters for beta distribution... |
| cov_beta | covariance matrix of betas for an ld block 'cov_beta' |
| create_basis | This function creates a basis 'create_basis' creates a trait... |
| create_ds_matrix | This function creates a trait snp matrix 'create_ts_matrix'... |
| e_lor | This function computes expected log odds ratio for a set of... |
| est_a1b1 | This function estimates shape parameters for a prior... |
| flip_allele | 'align_allele' given a data.table of pid,a1,a2 get a list of... |
| fopt | This function computes the optimal shape parameter a1 for a... |
| get_gwas_data | 'get_gwas_data' integrate GWAS summary data with support... |
| get_seb | An internal helper function to get obtain standard error of... |
| LD | Burren sparse basis files |
| logsum | helper function to sum logs without loss of precision... |
| lor_constraint | This function computes a probability for a given... |
| lor_f | This function samples from the posterior distribution of a... |
| lyons_egpa | EGPA combined GWAS summary statistics |
| maf_se_estimate | Compute minor allele frequency shrinkage 'maf_se_estimate'... |
| maf_se_estimate_sample_size | Compute minor allele frequency shrinkage using sample size... |
| mvs_perm | Code to sample multivariate norm 'mvs_perm' sample from a... |
| mvs_sigma | Code to compute sigma - genotype covariance matrix... |
| opt_a1b1 | This function estimates shape parameters for a prior... |
| p2z | convert p value to a signed Z score 'p2z' p value to a signed... |
| post_lor | This function samples from the posterior distribution of... |
| project_basis | This function projects an aligned trait onto the basis... |
| project_sparse | A streamlined function to project a trait onto a sparse basis... |
| rot.pca | Burren sparse basis files |
| se_null | This function computes standard error under the null... |
| shrinkage | Burren sparse basis files |
| simulate_beta | simulate betas for an ld block 'simulate_beta' use the... |
| simulate_study | simulate betas for a study 'simulate_study' use the... |
| SNP.manifest | Burren sparse basis files |
| use.pca | Burren sparse basis files |
| vcf2snpmatrix | convert a vcf file to snpMatrix object 'vcf2snpmatrix'... |
| wakefield_null_pp | compute reciprocal posterior probabilities using Wakefield's... |
| wakefield_pp | compute posterior probabilities using Wakefield's approximate... |
| ws_shrinkage | This function computes an alternative to the Bayesian... |
| z2p | convert z to p value 'p2z' z to p value |
