R/data_docs.r

In alexandruioanvoda/gwascelltyper: Fast GWAS Enrichment Testing

#' Standard summstats column headers
#'
#' Equivalency table written by Nathan Skene et al. (2018) for their MAGMA.Celltyping package. Used to standardize GWAS summary statistics headers.
#'
#' @docType data
#'
#' @usage data(standard_sumstats_column_headers)
#'
#' @format An object of class \code{"data frame"}.
#'
#' @keywords standard sumstats column headers gwas
#'
#' @references 1. Nathan Skene et al. Nat. Genet. 2018.
#' (\href{https://www.ncbi.nlm.nih.gov/pubmed/29785013}{PubMed})
#'
#' @examples
#' data(standard_sumstats_column_headers)
#' head(standard_sumstats_column_headers)
#'
"standard_sumstats_column_headers"


#' SNP location data
#'
#' SNP location written by Nathan Skene et al. (2018) for their MAGMA.Celltyping package. Used to find rsIDs for SNPs when they're not present.
#'
#' @docType data
#'
#' @usage data(snp_loc)
#'
#' @format An object of class \code{"data frame"}.
#'
#' @keywords snp location gwas
#'
#' @references 1. Nathan Skene et al. Nat. Genet. 2018.
#' (\href{https://www.ncbi.nlm.nih.gov/pubmed/29785013}{PubMed})
#'
#' @examples
#' data(standard_sumstats_column_headers)
#' head(standard_sumstats_column_headers)
#'
"snp_loc"

#' Map from Entrez to HGNC
#'
#' Gene map from Entrez to HGNC, written by Nathan Skene et al. (2018) for their MAGMA.Celltyping package. Used to find rsIDs for SNPs when they're not present.
#'
#' @docType data
#'
#' @usage data(all_hgnc_wtEntrez)
#'
#' @format An object of class \code{"data frame"}.
#'
#' @keywords gene map entrez hgnc
#'
#' @references 1. Nathan Skene et al. Nat. Genet. 2018.
#' (\href{https://www.ncbi.nlm.nih.gov/pubmed/29785013}{PubMed})
#'
#' @examples
#' data(all_hgnc_wtEntrez)
#' head(all_hgnc_wtEntrez)
#'
"all_hgnc_wtEntrez"