Function reference • echodata

All functions
`BST1`	echolocatoR output example: BST1 locus
`BST1_LD_matrix`	LD with the lead SNP: BST1 locus
`LRRK2`	echolocatoR output example: LRRK2 locus
`MEX3C`	echolocatoR output example: MEX3C locus
`R.utils`	R.utils
`assign_lead_snp()`	Assign lead SNP
`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
`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_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_SNPgroup_counts()`	Get SNP group counts
`get_data()`	Get data
`get_header()`	Get file header
`get_nrows()`	Get nrows
`get_os()`	Get OS
`get_sample_size()`	Get sample size
`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
`melt_finemapping_results()`	Melt fine-mapping results
`merge_finemapping_results()`	Merge fine-mapping results from all loci
`merge_robust()`	Merge robust
`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
`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
`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
`unlist_dt()`	Unlist a data.table
`update_cols()`	Update CS cols
`write_parquet()`	Write parquet file

Reference

All functions