Files in RajLabMSSM/echodata

echoverse module: Fine-mapping data access and formatting

.Rbuildignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/rworkflows.yml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/assign_lead_SNP.R R/auto_topSNPs_sub.R R/biomart_geneInfo.R R/calculate_tstat.R R/column_dictionary.R R/construct_colmap.R R/coords_to_rsids.R R/createDT.R R/data.R R/detect_genes.R R/dt_to_granges.R R/example_fullSS.R R/extract_loci.R R/fillNA_CS_PP.R R/filter_snps.R R/find_consensus_snps.R R/find_consensus_snps_no_polyfun.R R/find_top_consensus.R R/fix_coltypes.R R/gene_locus_list.R R/gene_trimmer.R R/get_CS_bins.R R/get_CS_counts.R R/get_Kunkle2019.R R/get_Kunkle2019_coloc.R R/get_Nalls2019.R R/get_Nalls2019_coloc.R R/get_Nalls2019_loci.R R/get_Nalls2019_merged.R R/get_SNPgroup_counts.R R/get_data.R R/get_header.R R/get_nrows.R R/get_os.R R/get_sample_size.R R/granges_to_bed.R R/import_topSNPs.R R/import_topSNPs_manual_rename.R R/imports.R R/is_empty.R R/is_ggbio.R R/is_ggplot.R R/is_granges.R R/is_local.R R/is_melted.R R/is_url.R R/limit_snps.R R/melt_finemapping_results.R R/merge_finemapping_results.R R/merge_finemapping_results_each.R R/merge_robust.R R/message_parallel.R R/messager.R R/mungesumstats_check_syn.R R/mungesumstats_to_echolocatoR.R R/order_loci.R R/order_methods.R R/portal_metadata.R R/portal_query.R R/preview.R R/read_parquet.R R/reassign_lead_snps.R R/results_report.R R/set_permissions.R R/snp_group_colorDict.R R/snp_group_filters.R R/standardize.R R/standardize_1snp_per_coord.R R/standardize_a1_a2.R R/standardize_coltypes.R R/standardize_gene.R R/standardize_gene_col.R R/standardize_gene_locus_cols.R R/standardize_maf.R R/standardize_main_colnames.R R/standardize_ncas_ncon.R R/standardize_p.R R/standardize_proportion_cases.R R/standardize_stderr.R R/standardize_trimws.R R/topSNPs_reader.R R/unlist_dt.R R/update_cols.R R/write_parquet.R R/zzz.R README.Rmd README.md

data/BST1.rda

data/BST1_LD_matrix.rda

data/LRRK2.rda

data/MEX3C.rda

data/genome_wide_dir.rda

data/locus_dir.rda

data/sumstatsColHeaders.rda

data/topSNPs_Kunkle2019.rda

data/topSNPs_Nalls2019.rda

data/topSNPs_Nalls2019_raw.rda

inst/CITATION

inst/extdata/BST1.1KGphase3.vcf.bgz

inst/extdata/BST1.1KGphase3.vcf.bgz.tbi

inst/hex/hex.png

inst/hex/hexSticker.Rmd man/BST1.Rd man/BST1_LD_matrix.Rd man/LRRK2.Rd man/MEX3C.Rd man/R.utils.Rd man/assign_lead_SNP.Rd man/auto_topSNPs_sub.Rd man/biomart_geneInfo.Rd man/calculate_tstat.Rd man/column_dictionary.Rd man/construct_colmap.Rd man/coords_to_rsids.Rd man/createDT.Rd man/detect_genes.Rd man/dt_to_granges.Rd man/example_fullSS.Rd man/extract_loci.Rd man/fillNA_CS_PP.Rd man/filter_snps.Rd man/find_consensus_snps.Rd man/find_consensus_snps_no_polyfun.Rd man/find_top_consensus.Rd man/fix_coltypes.Rd man/gene_locus_list.Rd man/gene_trimmer.Rd man/genome_wide_dir.Rd man/get_CS_bins.Rd man/get_CS_counts.Rd man/get_Kunkle2019.Rd man/get_Kunkle2019_coloc.Rd man/get_Nalls2019.Rd man/get_Nalls2019_coloc.Rd man/get_Nalls2019_loci.Rd man/get_Nalls2019_merged.Rd man/get_SNPgroup_counts.Rd man/get_data.Rd man/get_header.Rd man/get_nrows.Rd man/get_os.Rd man/get_sample_size.Rd man/granges_to_bed.Rd man/import_topSNPs.Rd man/is_empty.Rd man/is_ggbio.Rd man/is_ggplot.Rd man/is_granges.Rd man/is_local.Rd man/is_url.Rd man/limit_snps.Rd man/locus_dir.Rd man/melt_finemapping_results.Rd man/merge_finemapping_results.Rd man/merge_finemapping_results_each.Rd man/merge_robust.Rd man/message_parallel.Rd man/mungesumstats_check_syn.Rd man/mungesumstats_to_echolocatoR.Rd man/order_loci.Rd man/portal_metadata.Rd man/portal_query.Rd man/preview.Rd man/read_parquet.Rd man/reassign_lead_snps.Rd man/results_report.Rd man/set_permissions.Rd man/snp_group_colorDict.Rd man/snp_group_filters.Rd man/standardize.Rd man/standardize_gene.Rd man/standardize_gene_locus_cols.Rd man/standardize_maf.Rd man/sumstatsColHeaders.Rd man/topSNPs_Kunkle2019.Rd man/topSNPs_Nalls2019.Rd man/topSNPs_Nalls2019_raw.Rd man/topSNPs_reader.Rd man/unlist_dt.Rd man/update_cols.Rd man/write_parquet.Rd tests/testthat.R tests/testthat/test-MUNGESUMSTATS.R tests/testthat/test-assign_lead_SNP.R tests/testthat/test-column_dictionary.R tests/testthat/test-construct_colmap.R tests/testthat/test-coords_to_rsids.R tests/testthat/test-createDT.R tests/testthat/test-dt_to_granges.R tests/testthat/test-example_fullSS.R tests/testthat/test-extract_loci.R tests/testthat/test-fillNA_CS_PP.R tests/testthat/test-filter_snps.R tests/testthat/test-find_consensus_SNPs.R tests/testthat/test-find_consensus_snps_no_polyfun.R tests/testthat/test-find_top_consensus.R tests/testthat/test-gene_locus_list.R tests/testthat/test-get_Nalls2019_loci.R tests/testthat/test-get_SNPgroup_counts.R tests/testthat/test-get_data.R tests/testthat/test-get_header.R tests/testthat/test-get_sample_size.R tests/testthat/test-granges_to_bed.R tests/testthat/test-import_topSNPs.R tests/testthat/test-is_empty.R tests/testthat/test-is_ggbio.R tests/testthat/test-is_ggplot.R tests/testthat/test-is_url.R tests/testthat/test-limit_snps.R tests/testthat/test-melt_finemapping_results.R tests/testthat/test-merge_finemapping_results.R tests/testthat/test-merge_robust.R tests/testthat/test-parquet.R tests/testthat/test-portal_query.R tests/testthat/test-preview.R tests/testthat/test-reassign_lead_snps.R tests/testthat/test-snp_group_colorDict.R tests/testthat/test-snp_group_filters.R tests/testthat/test-standardize.R tests/testthat/test-update_cols.R vignettes/echodata.Rmd vignettes/echolocatoR_Finemapping_Portal.Rmd

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.