All functions

BST1

echolocatoR output example (BST1 locus)

BST1__Alasoo_2018.macrophage_IFNg

eQTL Catalogue query results

LRRK2

echolocatoR output example (LRRK2 locus)

LRRK2__Alasoo_2018.macrophage_IFNg

eQTL Catalogue query results

MEX3C

echolocatoR output example (MEX3C locus)

MEX3C__Alasoo_2018.macrophage_IFNg

eQTL Catalogue query results

catalogueR-package

Rapid querying, colocalization, and plotting of summary stats from the eQTL Catalogue

coloc_QTLs

Example colocalization results

coloc_QTLs_full

Example colocalization results

eQTL_Catalogue.annotate_tissues()

Annotate QTL datasets with metadata

eQTL_Catalogue.fetch()

2. Query eQTL Catalogue datasets by region

eQTL_Catalogue.header

eQTL Catalogue tabix header

eQTL_Catalogue.iterate_fetch()

Iterate queries to eQTL Catalogue

eQTL_Catalogue.list_datasets()

List available eQTL datasets

eQTL_Catalogue.query()

Iterate queries to eQTL Catalogue

eQTL_Catalogue.search_metadata()

Search eQTL Catalogue metadata

ensembl_to_hgnc()

Convert ENSEMBL IDs to HGNC gene symbols

example_eQTL_Catalogue_query_paths()

Paths to example eQTL Catalogue query results

example_sumstats_paths()

Paths to example summary stats

fetch_restAPI()

2. Query eQTL Catalogue datasets by region

fetch_tabix()

2. Query eQTL Catalogue datasets by region

find_consensus_SNPs()

Find Consensus SNPs in echolocatoR output

gather_colocalized_data()

Prepare data for coloc plot

gather_files()

Merge files from a list of paths

get_colocs()

Run coloc on GWAS-QTL object

hgnc_to_ensembl()

Convert HGNC gene symbols to ENSEMBL IDs

liftover()

Lift genome across builds

merge_gwas_qtl()

Merge GWAS data (query) and QTL data (results)

meta

eQTL Catalogue dataset metadata

multi_locus_plot()

Faceted Manhattan plots of QTL datasets

plot_coloc_summary()

Plot summary of coloc tests

retrieve_sumstats_info()

Merge coloc results with SNP-wise GWAS/QTL data

run_coloc()

Iteratively run coloc on merged GWAS-QTL datatables