infer_ancestry: Infer ancestry of GWAS dataset by matching against 1000...
In MRCIEU/ieugwasr: Interface to the 'OpenGWAS' Database API
infer_ancestry R Documentation
Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies
Description
Uses ~20k SNPs selected for common frequency across 5 major super populations
Usage
infer_ancestry(d, snpinfo = NULL, opengwas_jwt = get_opengwas_jwt())
Arguments
d
Data frame containing at least rsid and eaf columns.
e.g. output from associations
snpinfo
Output from afl2_list, afl2_rsid or afl2_chrpos.
If NULL then afl2_list() is used by default
opengwas_jwt
Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
Value
data frame ordered by most likely ancestry, each row represents a super population and cor column represents the correlation between the GWAS dataset and the 1000 genomes super population allele frequencies
MRCIEU/ieugwasr documentation built on Aug. 22, 2024, 8:44 p.m.
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| infer_ancestry | R Documentation |
Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies
Description
Uses ~20k SNPs selected for common frequency across 5 major super populations
Usage
infer_ancestry(d, snpinfo = NULL, opengwas_jwt = get_opengwas_jwt())
Arguments
d |
Data frame containing at least |
snpinfo |
Output from |
opengwas_jwt |
Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT. |
Value
data frame ordered by most likely ancestry, each row represents a super population and cor column represents the correlation between the GWAS dataset and the 1000 genomes super population allele frequencies
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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