Man pages for RajLabMSSM/echoLD
echoverse module: LD downloading and processing
| check_population_1kg | Translate superpopulation acronyms |
| compute_LD | Get LD using 'snpStats' package |
| compute_LD_blocks | Compute LD blocks |
| download_UKB_LD | Download UKB LD |
| fill_NA | Fill NAs in an LD matrix |
| filter_LD | Filter LD |
| get_LD | Procure an LD matrix for fine-mapping |
| get_LD_1KG | Compute LD from 1000 Genomes |
| get_LD_1KG_download_vcf | Download VCF subset from 1000 Genomes |
| get_LD_blocks | Get LD blocks |
| get_LD_matrix | Get LD from pre-computed matrix |
| get_LD_UKB | Download LD matrices from UK Biobank |
| get_LD_vcf | Compute LD from VCF file |
| get_lead_r2 | Get LD with lead SNP |
| get_leadsnp_block | Get lead SNP block |
| get_locus_vcf_folder | Get VCF storage folder |
| get_MAF_UKB | Get MAF from UK Biobank. |
| ldlinkr_ldproxy_batch | Extract LD proxies from 1KGphase3 |
| message_parallel | Send messages to console even from within parallel processes |
| plot_LD | Plot a subset of the LD matrix |
| popDat_1KGphase1 | Population metadata: 1KGphase1 |
| popDat_1KGphase3 | Population metadata: 1KGphase3 |
| r2_to_r | Convert r^2 to r, and vice versa |
| rds_to_npz | Convert .RDS file back to .npz format |
| read_LD_list | Read LD list |
| readSparse | Read LD matrix |
| report_time | Report time at end of function |
| save_LD_matrix | Save LD matrix |
| saveSparse | Save LD matrix as a sparse matrix |
| select_vcf_samples | Subset VCF samples |
| snpstats_get_MAF | Get MAF using 'snpStats' package |
| source_all | source_all |
| subset_common_snps | Subset LD matrix and dataframe to only their shared SNPs |
| to_sparse | Convert to sparse |
| vcf_to_plink | Convert VCF to PLINK |
