Package index • tidyGWAS

tidyGWAS

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

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

meta_analyse(): Improved meta-analysis using tidyGWAS:ed files
create_lake(): Create a data lake in hivestyle format
deprec_meta_analyze(): Perform meta-analysis of GWAS summary statistics datasets cleaned by tidyGWAS This function is depreciated. Use meta_analyse()
align_to_ref(): Align EffectAllele to always be the reference genome allele
by_chrom(): Meta analyse a chromosome, one at a time!

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
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
repair_stats(): Repair statistics column in a GWAS summary statistics tibble
validate_sumstat(): Validate statistics columns in a GWAS summary statistics file