Man pages for RajLabMSSM/echodata
echoverse module: Fine-mapping data access and formatting
| assign_lead_SNP | Assign lead SNP |
| auto_topSNPs_sub | Automatically identify top SNP per locus |
| biomart_geneInfo | Get gene info using Biomart |
| BST1 | 'echolocatoR' output example: BST1 locus |
| BST1_LD_matrix | LD with the lead SNP: BST1 locus |
| calculate_tstat | Impute t-stat |
| column_dictionary | Map column names to positions. |
| construct_colmap | Target column map |
| coords_to_rsids | Get RSIDS from SNP coordinates |
| createDT | Interactive DT |
| detect_genes | Detect QTL genes in full summary stats file |
| dt_to_granges | Convert data.table to GRanges object |
| example_fullSS | Store 'fullSS_dat' |
| extract_loci | Extract loci from GWAS/QTL summary statistics |
| fillNA_CS_PP | Fill NAs in PP and CS columns |
| filter_snps | Filter SNPs |
| find_consensus_snps | Find Consensus SNPs |
| find_consensus_snps_no_polyfun | Find Consensus SNPs: without PolyFun |
| find_top_consensus | Find the top Consensus SNP |
| fix_coltypes | Automatically fix column types |
| gene_locus_list | Generate a named list of (e)Gene-Locus pairs |
| gene_trimmer | Remove all SNPs outside of of a given gene. |
| genome_wide_dir | Example results path for genome-wide results |
| get_CS_bins | Get Credible Set bins |
| get_CS_counts | Get Credible Set SNP counts |
| get_data | Get data |
| get_header | Get file header |
| get_Kunkle2019 | Example GWAS summary statistics: Kunkle2019 |
| get_Kunkle2019_coloc | Get colocalization results with Kunkle2019 GWAS |
| get_Nalls2019 | Example GWAS summary statistics: Nalls2019 |
| get_Nalls2019_coloc | Get colocalization results with Nalls2019 GWAS |
| get_Nalls2019_loci | 'echolocatoR' output example: select loci |
| get_Nalls2019_merged | 'echolocatoR' output example: all loci |
| get_nrows | Get nrows |
| get_os | Get OS |
| get_sample_size | Get sample size |
| get_SNPgroup_counts | Get SNP group counts |
| granges_to_bed | Convert from GRanges to BED format |
| import_topSNPs | Import top GWAS/QTL summary statistics |
| is_empty | Check if a file is empty |
| is_ggbio | Is an object of class ggbio |
| is_ggplot | Is an object of class ggplot |
| is_granges | Is an object of class GRanges |
| is_local | Is local |
| is_url | Check if the input is url e.g. http:// or ftp:// |
| limit_snps | Limit the number of SNPs per locus. |
| locus_dir | Example results path for 'Nall2019' BST1 locus |
| LRRK2 | 'echolocatoR' output example: LRRK2 locus |
| melt_finemapping_results | Melt fine-mapping results |
| merge_finemapping_results | Merge fine-mapping results from all loci |
| merge_finemapping_results_each | Create full cross-locus merged files for each dataset, then... |
| merge_robust | Merge robust |
| message_parallel | Send messages to console even from within parallel processes |
| MEX3C | 'echolocatoR' output example: MEX3C locus |
| mungesumstats_check_syn | Check colname synonyms |
| mungesumstats_to_echolocatoR | Convert from 'MungeSumstats' to 'echolocatoR' format |
| order_loci | Order loci |
| portal_metadata | Import metadata |
| portal_query | Search and download fine-mapping files |
| preview | Preview formatted sum stats saved to disk |
| read_parquet | Read parquet file |
| reassign_lead_snps | Reassign lead SNPs |
| results_report | Results report |
| R.utils | R.utils |
| set_permissions | Set permissions |
| snp_group_colorDict | Assign colors to each SNP group |
| snp_group_filters | Get SNP group filters |
| standardize | Standardize the locus subset |
| standardize_gene | Standardize genes |
| standardize_gene_locus_cols | Standardizse gene/locus columns |
| standardize_maf | Standardize MAF |
| sumstatsColHeaders | 'sumstatsColHeaders' from 'MungeSumstats' |
| topSNPs_Kunkle2019 | TopSS example file (processed): Kunkle2019 |
| topSNPs_Nalls2019 | TopSS example file (processed): Nalls2019 |
| topSNPs_Nalls2019_raw | TopSS example file: Nalls2019 |
| topSNPs_reader | Read in top SNPs |
| unlist_dt | Unlist a data.table |
| update_cols | Update CS cols |
| write_parquet | Write parquet file |
