R/gwas_catalog.R

In MRCIEU/MRInstruments: Data sources for genetic instruments to be used in MR

#' Data frame of GWAS significant SNPs obtained from the EBI GWAS catalog
#'
#' Downloaded from EBI on 18/03/2016.
#' Standardised to make units as consistent as possible, trait names, obtain gene annotation.
#' Effect sizes and standard errors are all converted to log odds ratio for binary traits.
#' Ensembl used to identify alleles and effect allele frequency where missing.
#'
#' @format A data frame with 22783 rows and 17 columns
#'	\describe{
#'       \item{Phenotype_simple}{Simple phenotype name}
#'       \item{Phenotype}{This phenotype also has units and details if they are necessary to distinguish different studies}
#'       \item{Phenotype_info}{Phenotype_info}
#'       \item{PubmedID}{PubmedID}
#'       \item{Author}{Author}
#'       \item{Year}{Year}
#'       \item{SNP}{SNP}
#'       \item{chr}{chr}
#'       \item{bp_ens_GRCh38}{bp_ens_GRCh38}
#'       \item{Region}{Region}
#'       \item{gene}{gene}
#'       \item{Gene_ens}{Gene_ens}
#'       \item{effect_allele}{effect_allele}
#'       \item{other_allele}{other_allele}
#'       \item{beta}{beta}
#'       \item{se}{se}
#'       \item{pval}{pval}
#'       \item{units}{units}
#'       \item{eaf}{eaf}
#'       \item{date_added_to_MRBASE}{Date GWAS catalog downloaded and added to MR-Base}
#'       \item{Initial_sample_description}{Sample size and ancestry description for stage 1 of GWAS (summing across multiple Stage 1 populations, if applicable)}
#'       \item{Replication_sample_description}{Sample size and ancestry description for subsequent replication(s) (summing across multiple populations, if applicable)}
#'       \item{MAPPED_TRAIT_EFO_URI}{URI of the EFO trait}
#'       \item{MAPPED_TRAIT_EFO}{Mapped Experimental Factor Ontology trait for this study}
#'       \item{STUDY.ACCESSION}{Accession ID allocated to a GWAS Catalog study}
#'	}
#'
#' @source \url{https://scmv-ieugit.epi.bris.ac.uk/gh13047/gwas_catalog_standardisation}
"gwas_catalog"