Every rsid is searched for against each requested GWAS id. To get a list of
available GWAS ids, or to find their meta data, use gwasinfo
.
Can request LD proxies for instances when the requested rsid is not present
in a particular GWAS dataset. This currently only uses an LD reference panel
composed of Europeans in 1000 genomes version 3.
It is also restricted to biallelic single nucleotide polymorphisms (no indels),
with European MAF > 0.01.
Usage
associations(
variants,
id,
proxies = 1,
r2 = 0.8,
align_alleles = 1,
palindromes = 1,
maf_threshold = 0.3,
access_token = check_access_token()
)
Arguments
- variants
Array of variants e.g.
c("rs234", "7:105561135-105563135")
- id
Array of GWAS studies to query. See
gwasinfo
for available studies- proxies
0
or (default)1
- indicating whether to look for proxies- r2
Minimum proxy LD rsq value. Default=
0.8
- align_alleles
Try to align tag alleles to target alleles (if
proxies = 1
).1
= yes (default),0
= no- palindromes
Allow palindromic SNPs (if
proxies = 1
).1
= yes (default),0
= no- maf_threshold
MAF threshold to try to infer palindromic SNPs. Default =
0.3
.- access_token
Google OAuth2 access token. Used to authenticate level of access to data. By default, checks if already authenticated through
get_access_token
and if not then does not perform authentication