R/getScores.R

In rmsharp/parentfindr: What the Package Does (One Line, Title Case)

#' Get all of the \code{missing}, \code{invalid}, and \code{descrepant} loci
#' scores.
#'
#' @return A list containing a named list for each offspring.
#' The name of each list is the offspring's animal ID.
#' Within each offspring list is a list of potential dams and each of those
#' lists is named using the potential dam's ID.
#' The dam's list contains the following data.
#'
#' \enumerate{
#' \item{\code{refId}} {The ID of the offspring}
#' \item{\code{parentSex}} {The sex of the potential dam, which should always
#' be "F".}
#' \item{\code{missingLoci}} {The number of missing loci, which are the loci
#' without genotypes in the parent.}
#' \item{\code{invalidLoci}} {The number of invalid loci, which are the loci
#' missing in the offspring but present in the parent.}
#' \item{\code{discrepantLoci}} {The number of discrepant loci, the
#' non-matching loci
#' in the parent in offspring where both have genotypes.}
#' \item{\code{numLociCompared}} {The number of loci compared}
#' \item{\code{fractionNonDiscrepant}} {The fraction of non-discrepant loci,
#' which is
#' the ratio of (\code{numLociCompared} - \code{discrepantLoci}) /
#' \code{numLociCompared}.}
#' \item{\code{pkMatch}} {A list with the following three elements.
#'     \itemize{
#'     \item{\code{kid}} {The ID of the offspring}
#'     \item{\code{pkLMatch}} {A logical vector representing the concordance
#'     (\code{TRUE}) or non-concordance \code{FALSE} between the kid and
#'     dam's left allele (\code{pkLMatch})}
#'     \item{\code{pkRMatch}} {A logical vector representing the concordance
#'     (\code{TRUE}) or non-concordance \code{FALSE} between the kid and
#'     dam's right allele (\code{pkRMatch}).}
#'     }
#'  }
#'  \item{\code{text}} {A character vector describing each discrepant record.
#'  Each element contains the name of the discrepant locus, the offspring's
#'  genotype and the dam's genotype.}
#'  \item{\code{sires}} {A list of potential sires nested within the current
#'  dam of the list of dams nested inside the current offspring.
#'  Each sire is represented with
#'  a named list with the sire ID as the name of the list and the contents of
#'  the list are as follows:
#'     \enumerate{
#'     \item{\code{refId}} {The offspring ID}
#'     \item{\code{parentSex}} {Sex of the sire, which should always be "M"}
#'     \item{\code{missingLoci}} {The number of missing loci, which are the
#'     loci
#'     without genotypes in the parent.}
#'     \item{\code{invalidLoci}} {The number of invalid loci, which are the
#'     loci missing
#'     in the offspring but present in the parent.}
#'     \item{\code{discrepantLoci}} {The number of discrepant loci, the
#'     non-matching loci
#'     in the parent in offspring where both have genotypes.}
#'     \item{\code{numLociCompared}} {The number of loci compared}
#'     \item{\code{fractionNonDiscrepant}} {The fraction of non-discrepant
#'     loci, which is
#'     the ratio of (\code{numLociCompared} - \code{discrepantLoci}) /
#'     \code{numLociCompared}.}
#'     \item{\code{pkMatch}} {A list with the following three elements.
#'         \itemize{
#'         \item{\code{kid}} {The ID of the offspring}
#'         \item{\code{pkLMatch}} {A logical vector representing the concordance
#'         (\code{TRUE}) or non-concordance \code{FALSE} between the kid and
#'         dam's left allele (\code{pkLMatch})}
#'         \item{\code{pkRMatch}} {A logical vector representing the concordance
#'         (\code{TRUE}) or non-concordance \code{FALSE} between the kid and
#'         dam's right allele (\code{pkRMatch}).}
#'         }
#'        }
#'     \item{\code{text}} {A character vector describing each discrepant record.
#'     Each element contains the name of the discrepant locus, the offspring's
#'     genotype and the sire's genotype.}
#'     }
#'   }
#' }
#' @param trios List containing a list for each offspring. Each offspring list
#' contains a named character vector of length one (\code{offspring}) containing
#' the offspring ID, a character vector of potential dams (\code{dams}),
#' and a named character vector of potential sires (\code{sires}).
#' @param animalAlleles List with all allele information for all animals.
#' @export
getScores <- function(trios, animalAlleles) {
  allScores <- list()
  for (kidId in names(trios)) {
    allScores[[kidId]] <- collectTrioScores(kidId, trios[[kidId]]$dams,
                                            trios[[kidId]]$sires, animalAlleles)
  }
  allScores
}