GitHub - MRCIEU/MRInstruments: Data objects for various sets of instruments (original) (raw)

MRInstruments

This is an R package that contains a number of data files from various sources to provide instruments in two sample MR. To install this package use:

devtools::install_github("MRCIEU/MRInstruments") library(MRInstruments)

For more information about performing two sample MR see https://github.com/MRCIEU/TwoSampleMR

Contents

• aries_mqtl: https://scmv-ieugit.epi.bris.ac.uk/gh13047/aries_mqtl_catalog
• drug_interactions: https://scmv-ieugit.epi.bris.ac.uk/gh13047/gtex_data
• gene_trials: https://scmv-ieugit.epi.bris.ac.uk/gh13047/gtex_data
• gtex_eqtl: https://scmv-ieugit.epi.bris.ac.uk/gh13047/gtex_data
• gwas_catalog: https://scmv-ieugit.epi.bris.ac.uk/gh13047/gwas_catalog_standardisation
• proteomic_qtls: https://scmv-ieugit.epi.bris.ac.uk/gh13047/proteomic_qtls
• metab_qtls: https://scmv-ieugit.epi.bris.ac.uk/gh13047/metabolomic_qtls

Maintenance

To add a dataset copy to /data as a .RData file, and create a corresponding .R file in /R to enter the documentation for the data. For example, the GTEx data set is documented like this in the R/eqtl_mrbase.R file:

#' Data frame of eQTLs from GTEx study #' #' A total of 273700 Gene expression - SNP associations from 27094 gene names and 44 tissues. Obtained from \url{http://www.gtexportal.org/home/}. #' These data only include associations that GTEx labelled as \code{is_choson_snp}. #' Where available, genes that are used as drug targets are annotated #' The drug information comes from PMID 26121088 #' #' @format A data frame with 273700 rows and 16 columns #' \describe{ #' \item{gene_name}{Gene name} #' \item{tissue}{Tissue} #' \item{gene_start}{Gene chromosome : gene start position (b37)} #' \item{SNP}{SNP rs ID} #' \item{snp_position}{SNP chromosome : SNP position (b37)} #' \item{effect_allele}{Effect allele} #' \item{other_allele}{Non effect allele} #' \item{beta}{Effect size} #' \item{se}{Standard error} #' \item{P_value}{p-value} #' \item{n}{samplesize} #' \item{drug_proxy}{Binary value for whether used as drug proxy} #' \item{MeSH1}{MeSH term 1} #' \item{MeSH2}{Top MeSH term} #' \item{drug_phase}{Phase of drug development} #' \item{approved}{Approved in EU or US} #' } #' #' @source \url{https://scmv-ieugit.epi.bris.ac.uk/gh13047/gtex_data} eqtl_mrbase

Please try to follow this convention for naming columns:

phenotype_col="Phenotype"
snp_col="SNP"
beta_col="beta"
se_col="se"
eaf_col="eaf"
effect_allele_col="effect_allele"
other_allele_col="other_allele"
pval_col="pval"
units_col="units"
ncase_col="ncase"
ncontrol_col="ncontrol"
samplesize_col="samplesize"
gene_col="gene"