Package index • tidyGWAS

tidyGWAS

Functions using dbSNP reference data

tidyGWAS(): Execute validation and quality control of GWAS summmary statistics

validate_rsid(): Validate format of the RSID column in a GWAS summary statistics file

infer_build(): Infer what genome build a GWAS summary statistics file is on.

repair_ids(): Augment a data.frame with information from dbSNP

set_default_dbsnp_path(): Save the filepath for the dbSNP reference data

Interact with GWAS catalog and Open Targets

from_gwas_catalog(): Download summary statistics from GWAS catalog

from_gwas_catalog_region(): Query a specific region of interest for a using a gwas catalog study_id

get_open_targets_cs(): Query Open targets for all credible sets containing the variant

check_rest_avail(): Check if API access is available for a GWAS catalog study

Validating columns

repair_stats(): Repair statistics column in a GWAS summary statistics tibble

validate_sumstat(): Validate statistics columns in a GWAS summary statistics file

Meta-analysis

meta_analyze(): Perform meta-analysis of GWAS summary statistics datasets cleaned by tidyGWAS

meta_analyze_by_chrom(): meta_analyze summary statistics, one chromosome at a time! This function is exposed to allow for testing using real data

Helpful functions

flag_duplicates(): Find all rows which are part of a set of duplicated rows

flag_indels(): Detect "indels" in GWAS summary statistics

flag_invalid_rsid(): Detect entries that are not valid rsID's in GWAS summary statistics

strand_flip(): Strand flip alleles

create_lake(): Create a data lake in hivestyle format