Man pages for alexandruioanvoda/gwascelltyper
Fast GWAS Enrichment Testing
| all_hgnc_wtEntrez | Map from Entrez to HGNC |
| bin_specificity_into_quantiles | Bin specificity into quantiles |
| compute_bjk_enrichment_discrete | Complete block jackknife joint test |
| compute_ewce_scores_environ | Compute EWCE scores - from environment-stored expression data |
| compute_ewce_selection_environ | Compute top N% EWCE gene-sets - from environment-stored... |
| compute_LDSC_enrichment_discrete | Compute LDSC enrichment |
| compute_LDSC_enrichment_discrete_optimized | Compute LDSC enrichment - optimized |
| compute_MAGMA_enrichment_discrete | Compute MAGMA enrichment |
| compute_MAGMA_enrichment_linear | Compute MAGMA enrichment linear |
| compute_SNPSEA_enrichment_discrete | Compute SNPsea enrichment linear |
| compute_SNPSEA_enrichment_linear | Compute SNPsea enrichment linear |
| compute_t_stat_matrix_environ | Compute t-stat matrix - from environment-stored expression... |
| compute_t_stat_scores_environ | Compute t-statistic scores - from environment-stored... |
| compute_t_stat_selection_environ | Compute top N% t-statistic gene-sets - from... |
| dep_path | Dependency data paths |
| download_dependencies | Download dependencies |
| exp_environ_missingness | Expression matrix (in environ object) missingness evaluation |
| finalStep_bjk_joint_test | Compute the block jackknife joint test discrete |
| find_magma_version | Find version of MAGMA binary |
| format_celltype_names | Format celltype names |
| gene_object_renamer | Gene object renamer |
| generate_celltype_data_environ | Compute EWCE matrix - from environment-stored expression data |
| get_genomebuild_for_sumstats | Get genome build from sumstats |
| get_magma_paths | Get MAGMA paths |
| get_os | Detect OS |
| gwascelltyper | gwascelltyper |
| make_geneset_from_score_matrix | Make gene-set from gene-by-celltype specificity matrix |
| map_SNPs_to_genes_for_MAGMA | Map SNPs to genes for MAGMA |
| matrix_missingness | Matrix missingness evaluation |
| munge_sumstats_for_LDSC_from_MAGMA | Process summary statistics for LDSC |
| munge_sumstats_for_MAGMA | Process summary statistics for MAGMA |
| munge_sumstats_for_SNPSEA_from_MAGMA | Process summary statistics for SNPsea |
| range01 | Scale matrix between 0 and 1. |
| read_exp_and_annot_environ | Read exp and annot |
| sanity_check_for_exp_and_annot_environ | Sanity checking exp-annot correspondence |
| snp_loc | SNP location data |
| standard_sumstats_column_headers | Standard summstats column headers |
