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class-releases.R
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class-releases.R
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setOldClass(c("tbl_df", "tbl", "data.frame"))
#' An S4 class to represent a set of PGS Catalog Releases
#'
#' The releases object consists of four tables (slots) that combined form a
#' relational database of a subset of PGS Catalog releases. Each release is an
#' observation (row) in the \code{releases} table (first table).
#'
#' @slot releases A table of PGS Catalog releases. Each release (row) is
#' uniquely identified by the release date (\code{date}). Columns:
#' \describe{
#' \item{date}{Release date.}
#' \item{n_pgs}{Number of newly released Polygenic Scores.}
#' \item{n_ppm}{Number of newly released PGS Performance Metrics.}
#' \item{n_pgp}{Number of newly released PGS Publications.}
#' }
#' @slot pgs_ids A table of released Polygenic Scores (PGS) identifiers.
#' Columns:
#' \describe{
#' \item{date}{Release date.}
#' \item{pgs_id}{Polygenic Score (PGS) identifier. Example: \code{"PGS000001"}.}
#' }
#' @slot ppm_ids A table of the released PGS Performance Metrics identifiers.
#' Columns:
#' \describe{
#' \item{date}{Release date.}
#' \item{ppm_id}{A PGS Performance Metrics identifier. Example: \code{"PPM000001"}.}
#' }
#' @slot pgp_ids A table of the released PGS Publication identifiers. Columns:
#' \describe{
#' \item{date}{Release date.}
#' \item{pgp_id}{PGS Publication identifier. Example: \code{"PGP000001"}.}
#' }
#' @export
setClass(
"releases",
slots = c(
releases = "tbl_df",
pgs_ids = "tbl_df",
ppm_ids = "tbl_df",
pgp_ids = "tbl_df"
)
)
#' Constructor for the S4 releases object.
#'
#' Constructor for the S4 \linkS4class{releases} object.
#'
#' @param releases A \code{s4releases_releases_tbl} tibble.
#' @param pgs_ids A \code{s4releases_pgs_ids_tbl} tibble.
#' @param ppm_ids A \code{s4releases_ppm_ids_tbl} tibble.
#' @param pgp_ids A \code{s4releases_pgp_ids_tbl} tibble.
#'
#' @return An object of class \linkS4class{releases}.
#' @keywords internal
releases <-
function(releases = s4releases_releases_tbl(),
pgs_ids = s4releases_pgs_ids_tbl(),
ppm_ids = s4releases_ppm_ids_tbl(),
pgp_ids = s4releases_pgp_ids_tbl()) {
s4_releases <- methods::new(
"releases",
releases = releases,
pgs_ids = pgs_ids,
ppm_ids = ppm_ids,
pgp_ids = pgp_ids
)
return(s4_releases)
}
s4releases_releases_tbl <- function(date = lubridate::ymd(),
n_pgs = n_pgs,
n_ppm = n_ppm,
n_pgp = n_pgp,
notes = notes) {
tbl <- tibble::tibble(
date = date,
n_pgs = n_pgs,
n_ppm = n_ppm,
n_pgp = n_pgp,
notes = notes
)
return(tbl)
}
s4releases_pgs_ids_tbl <- function(date = lubridate::ymd(),
pgs_id = character()) {
tbl <- tibble::tibble(date = date,
pgs_id = pgs_id)
return(tbl)
}
s4releases_ppm_ids_tbl <- function(date = lubridate::ymd(),
ppm_id = character()) {
tbl <- tibble::tibble(date = date,
ppm_id = ppm_id)
return(tbl)
}
s4releases_pgp_ids_tbl <- function(date = lubridate::ymd(),
pgp_id = character()) {
tbl <- tibble::tibble(date = date,
pgp_id = pgp_id)
return(tbl)
}
coerce_to_s4_releases <- function(lst_tbl = NULL) {
if (is.null(lst_tbl)) {
s4_releases <- releases()
return(s4_releases)
}
s4_releases <- releases(
releases = lst_tbl$releases,
pgs_ids = lst_tbl$pgs_ids,
ppm_ids = lst_tbl$ppm_ids,
pgp_ids = lst_tbl$pgp_ids
)
s4_releases@releases <- drop_metadata_cols(s4_releases@releases)
s4_releases@pgs_ids <- drop_metadata_cols(s4_releases@pgs_ids)
s4_releases@ppm_ids <- drop_metadata_cols(s4_releases@ppm_ids)
s4_releases@pgp_ids <- drop_metadata_cols(s4_releases@pgp_ids)
return(s4_releases)
}