find_sumstats: Search Open GWAS for datasets matching criteria

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Search Open GWAS for datasets matching criteria

Description

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.

Usage

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

Details

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

Value

(Filtered) GWAS metadata table.

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)
)
}

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.