Files in RajLabMSSM/echoLD

echoverse module: LD downloading and processing

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md NEWS.md R/LD_1KG_download_vcf.R R/LD_reference_options.R R/UKB_find_ld_prefix.R R/check_LD_reference_1kg.R R/clean_UKB_tmps.R R/compute_LD.R R/compute_LD_blocks.R R/data.R R/download_UKB_LD.R R/fill_NA.R R/filter_LD.R R/get_1KG_url.R R/get_LD.R R/get_LD_1KG.R R/get_LD_UKB.R R/get_LD_blocks.R R/get_LD_matrix.R R/get_LD_vcf.R R/get_MAF_UKB.R R/get_lead_r2.R R/get_leadsnp_block.R R/get_locus_vcf_folder.R R/get_rds_path.R R/is_sparse_matrix.R R/ldlinkr_ldproxy_batch.R R/load_ld_r.R R/message_parallel.R R/messager.R R/plot_LD.R R/r2_to_r.R R/rds_to_npz.R R/readSparse.R R/read_LD_list.R R/report_time.R R/saveSparse.R R/save_LD_matrix.R R/select_vcf_samples.R R/snpstats_ensure_nonduplicates.R R/snpstats_get_MAF.R R/source_all.R R/subset_common_snps.R R/to_sparse.R R/translate_population.R R/vcf_to_plink.R R/zzz.R README.Rmd README.md inst/R_cli/LD_blocks_plink.R inst/R_cli/LD_clumping.R inst/R_cli/LD_custom_cli.R inst/R_cli/compute_LD_plink.R inst/R_cli/determine_chrom_type_vcf.R inst/R_cli/dprime_table_cli.R inst/R_cli/filter_vcf_cli.R inst/R_cli/filter_vcf_gaston.R inst/R_cli/index_vcf_cli.R inst/R_cli/leadsnp_block_plink.R inst/R_cli/plink_LD.R inst/R_cli/plink_file.R inst/R_cli/plink_to_snpstats.R inst/R_cli/query_vcf_cli.R inst/R_cli/read_bin.R inst/R_cli/read_ld_table.R inst/R_cli/run_plink_LD.R inst/R_cli/vcf_cleaning.R inst/R_cli/vcf_to_bed_cli.R inst/hex/hexSticker.Rmd man/check_population_1kg.Rd man/compute_LD.Rd man/compute_LD_blocks.Rd man/download_UKB_LD.Rd man/fill_NA.Rd man/filter_LD.Rd man/get_LD.Rd man/get_LD_1KG.Rd man/get_LD_1KG_download_vcf.Rd man/get_LD_UKB.Rd man/get_LD_blocks.Rd man/get_LD_matrix.Rd man/get_LD_vcf.Rd man/get_MAF_UKB.Rd man/get_lead_r2.Rd man/get_leadsnp_block.Rd man/get_locus_vcf_folder.Rd man/ldlinkr_ldproxy_batch.Rd man/message_parallel.Rd man/plot_LD.Rd man/popDat_1KGphase1.Rd man/popDat_1KGphase3.Rd man/r2_to_r.Rd man/rds_to_npz.Rd man/readSparse.Rd man/read_LD_list.Rd man/report_time.Rd man/saveSparse.Rd man/save_LD_matrix.Rd man/select_vcf_samples.Rd man/snpstats_get_MAF.Rd man/source_all.Rd man/subset_common_snps.Rd man/to_sparse.Rd man/vcf_to_plink.Rd tests/testthat.R tests/testthat/test-LD_1KG_download_vcf.R tests/testthat/test-filter_LD.R tests/testthat/test-get_LD.R tests/testthat/test-get_LD_matrix.R tests/testthat/test-get_LD_vcf.R tests/testthat/test-get_MAF_UKB.R tests/testthat/test-get_lead_r2.R tests/testthat/test-plot_LD.R tests/testthat/test-r2_to_r.R tests/testthat/test-readSparse.R tests/testthat/test-select_vcf_samples.R tests/testthat/test-subset_common_snps.R tests/testthat/test-vcf_to_plink.R vignettes/echoLD.Rmd