Supply the output from read_exposure_data()
and all the SNPs therein will be queried against the requested outcomes in remote database using API.
extract_outcome_data.Rd
Supply the output from read_exposure_data()
and all the SNPs therein will be queried against the requested outcomes in remote database using API.
Usage
extract_outcome_data(
snps,
outcomes,
proxies = TRUE,
rsq = 0.8,
align_alleles = 1,
palindromes = 1,
maf_threshold = 0.3,
access_token = ieugwasr::check_access_token(),
splitsize = 10000,
proxy_splitsize = 500
)
Arguments
- snps
Array of SNP rs IDs.
- outcomes
Array of IDs (see
id
column in output fromavailable_outcomes()
).- proxies
Look for LD tags? Default is
TRUE
.- rsq
Minimum LD rsq value (if proxies = 1). Default =
0.8
.- align_alleles
Try to align tag alleles to target alleles (if proxies = 1).
1
= yes,0
= no. The default is1
.- palindromes
Allow palindromic SNPs (if proxies = 1).
1
= yes,0
= no. The default is1
.- maf_threshold
MAF threshold to try to infer palindromic SNPs. The default is
0.3
.- access_token
Google OAuth2 access token. Used to authenticate level of access to data.
- splitsize
The default is
10000
.- proxy_splitsize
The default is
500
.