R/PheGWASData.R

In georgeg0/PheGWAS: R package to do many-variant many-phenotype association

#' HDL GWAS summary dataset (made available from Lipid consortium data files)
#'
#' The dataset 'hdl' is a data.frame object with the summary results of a GWAS analysis.
#'
#' @docType data
#'
#' @usage data(hdl)
#'
#' @format A dataframe with simulated GWAS results (simulated using plink 1.9)
#' \itemize{
#'   \item CHR is the chromosome number
#'   \item BP is the position of the chromosome
#'   \item rsid The SNP ID associated with that position and chromsome
#'   \item HDL is the p_value of the trait
#'   \item gene is the gene associated with rsid
#' }
#'
#' @keywords datasets
#' @return A data frame
#'
"hdl"

#' LDL GWAS summary dataset (made available from Lipid consortium data files)
#'
#' The dataset 'ldl' is a data.frame object with the summary results of a GWAS analysis.
#'
#' @docType data
#'
#' @usage data(ldl)
#'
#' @format A dataframe with simulated GWAS results (simulated using plink 1.9)
#' \itemize{
#'   \item CHR is the chromosome number
#'   \item BP is the position of the chromosome
#'   \item rsid The SNP ID associated with that position and chromsome
#'   \item LDL is the p_value of the trait
#'   \item gene is the gene associated with rsid
#' }
#'
#' @keywords datasets
#' @return A data frame
#'
"ldl"

#' TRIG GWAS summary dataset (made available from Lipid consortium data files)
#'
#' The dataset 'ldl' is a data.frame object with the summary results of a GWAS analysis.
#'
#' @docType data
#'
#' @usage data(trig)
#'
#' @format A dataframe with simulated GWAS results (simulated using plink 1.9)
#' \itemize{
#'   \item CHR is the chromosome number
#'   \item BP is the position of the chromosome
#'   \item rsid The SNP ID associated with that position and chromsome
#'   \item TRIGS is the p_value of the trait
#'   \item gene is the gene associated with rsid
#' }
#'
#' @keywords datasets
#' @return A data frame
#'
"trig"

#' TOTAL CHOLESTROL GWAS summary dataset (made available from Lipid consortium data files)
#'
#' The dataset 'tchol' is a data.frame object with the summary results of a GWAS analysis.
#'
#' @docType data
#'
#' @usage data(tchol)
#'
#' @format A dataframe with simulated GWAS results (simulated using plink 1.9)
#' \itemize{
#'   \item CHR is the chromosome number
#'   \item BP is the position of the chromosome
#'   \item rsid The SNP ID associated with that position and chromsome
#'   \item TOTAL_CHOLESTROL is the p_value of the trait
#'   \item gene is the gene associated with rsid
#' }
#'
#' @keywords datasets
#' @return A data frame
#'
"tchol"