Package index • echodata

Data access

Download and access example GWAS summary statistics and portal data.

get_data(): Get data
get_Nalls2019(): Example GWAS summary statistics: Nalls2019
get_Nalls2019_loci(): echolocatoR output example: select loci
get_Nalls2019_merged(): echolocatoR output example: all loci
get_Nalls2019_coloc(): Get colocalization results with Nalls2019 GWAS
get_Kunkle2019(): Example GWAS summary statistics: Kunkle2019
get_Kunkle2019_coloc(): Get colocalization results with Kunkle2019 GWAS
example_fullSS(): Store fullSS_dat
portal_metadata(): Import metadata
portal_query(): Search and download fine-mapping files

Data processing

Standardize, format, and import summary statistics.

standardize(): Standardize the locus subset
standardize_gene(): Standardize genes
construct_colmap(): Target column map
column_dictionary(): Map column names to positions.
import_topSNPs(): Import top GWAS/QTL summary statistics
mungesumstats_to_echolocatoR(): Convert from MungeSumstats to echolocatoR format
extract_loci(): Extract loci from GWAS/QTL summary statistics
fix_coltypes(): Automatically fix column types
update_cols(): Update CS cols
get_header(): Get file header
get_nrows(): Get nrows
get_sample_size(): Get sample size
coords_to_rsids(): Get RSIDS from SNP coordinates

Fine-mapping results

Process, merge, and summarize fine-mapping results.

find_consensus_snps(): Find Consensus SNPs
find_consensus_snps_no_polyfun(): Find Consensus SNPs: without PolyFun
find_top_consensus(): Find the top Consensus SNP
merge_finemapping_results(): Merge fine-mapping results from all loci
melt_finemapping_results(): Melt fine-mapping results
results_report(): Results report
fillNA_CS_PP(): Fill NAs in PP and CS columns
get_CS_bins(): Get Credible Set bins
get_CS_counts(): Get Credible Set SNP counts
get_SNPgroup_counts(): Get SNP group counts
filter_snps(): Filter SNPs
limit_snps(): Limit the number of SNPs per locus.
snp_group_filters(): Get SNP group filters
snp_group_colorDict(): Assign colors to each SNP group
assign_lead_snp(): Assign lead SNP
reassign_lead_snps(): Reassign lead SNPs

Utilities

General-purpose helper functions.

is_granges(): Is an object of class GRanges
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_local(): Is local
is_url(): Check if the input is url e.g. http:// or ftp://
dt_to_granges(): Convert data.table to GRanges object
granges_to_bed(): Convert from GRanges to BED format
merge_robust(): Merge robust
unlist_dt(): Unlist a data.table
createDT(): Interactive DT
preview(): Preview formatted sum stats saved to disk
detect_genes(): Detect QTL genes in full summary stats file
gene_locus_list(): Generate a named list of (e)Gene-Locus pairs
order_loci(): Order loci
get_os(): Get OS
set_permissions(): Set permissions
read_parquet(): Read parquet file
write_parquet(): Write parquet file

Bundled datasets

Pre-computed example datasets included with the package.

BST1: echolocatoR output example: BST1 locus
LRRK2: echolocatoR output example: LRRK2 locus
MEX3C: echolocatoR output example: MEX3C locus
BST1_LD_matrix: LD with the lead SNP: BST1 locus
topSNPs_Nalls2019: TopSS example file (processed): Nalls2019
topSNPs_Nalls2019_raw: TopSS example file: Nalls2019
topSNPs_Kunkle2019: TopSS example file (processed): Kunkle2019
locus_dir: Example results path for Nall2019 BST1 locus
genome_wide_dir: Example results path for genome-wide results
sumstatsColHeaders: sumstatsColHeaders from MungeSumstats

Other

R.utils: R.utils