Search Open GWAS for datasets matching criteria

For each argument, searches for any datasets matching a case-insensitive substring search in the respective metadata column. Users can supply a single character string or a list/vector of character strings.

find_sumstats(
  ids = NULL,
  traits = NULL,
  years = NULL,
  consortia = NULL,
  authors = NULL,
  populations = NULL,
  categories = NULL,
  subcategories = NULL,
  builds = NULL,
  pmids = NULL,
  min_sample_size = NULL,
  min_ncase = NULL,
  min_ncontrol = NULL,
  min_nsnp = NULL,
  include_NAs = FALSE,
  access_token = check_access_token()
)

Arguments

ids

List of Open GWAS study IDs (e.g. c("prot-a-664", "ieu-b-4760")).

traits

List of traits (e.g. c("parkinson", "Alzheimer")).

years

List of years (e.g. seq(2015,2021) or c(2010, 2012, 2021)).

consortia

List of consortia (e.g. c("MRC-IEU","Neale Lab").

authors

List of authors (e.g. c("Elsworth","Kunkle","Neale")).

populations

List of populations (e.g. c("European","Asian")).

categories

List of categories (e.g. c("Binary","Continuous","Disease","Risk factor"))).

subcategories

List of categories (e.g. c("neurological","Immune","cardio"))).

builds

List of genome builds (e.g. c("hg19","grch37")).

pmids

List of PubMed ID (exact matches only) (e.g. c(29875488, 30305740, 28240269)).

min_sample_size

Minimum total number of study participants (e.g. 5000).

min_ncase

Minimum number of case participants (e.g. 1000).

min_ncontrol

Minimum number of control participants (e.g. 1000).

min_nsnp

Minimum number of SNPs (e.g. 200000).

include_NAs

Include datasets with missing metadata for size criteria (i.e. min_sample_size, min_ncase, or min_ncontrol).

access_token

Google OAuth2 access token. Used to authenticate level of access to data

Value

(Filtered) GWAS metadata table.

Details

By default, returns metadata for all studies currently in Open GWAS database.

Examples

# Only run the examples if user has internet access:
if(try(is.character(getURL("www.google.com")))==TRUE){
### By ID
metagwas <- find_sumstats(ids = c(
    "ieu-b-4760",
    "prot-a-1725",
    "prot-a-664"
))
### By ID amd sample size
metagwas <- find_sumstats(
    ids = c("ieu-b-4760", "prot-a-1725", "prot-a-664"),
    min_sample_size = 5000
)
### By criteria
metagwas <- find_sumstats(
    traits = c("alzheimer", "parkinson"),
    years = seq(2015, 2021)
)
}
#> Error in getURL("www.google.com") : could not find function "getURL"