R/data.R

In KLINK: Kinship Analysis with Linked Markers

#' Built-in linkage map
#'
#' A genetic map including 50 autosomal STR markers.
#'
#' @format A data frame with 50 rows and 4 columns: `Marker`, `Chr`, `cM`,
#'   `Kit`.
#'
"LINKAGEMAP"


#' Dataset for a paternity case
#'
#' A list of two pedigrees forming the hypotheses in a paternity case: H1 (`AF`
#' is the father of `CH`) and H2 (unrelated). `AF` and `CH` are genotyped with
#' 11 markers, with allele frequencies from `norSTR::norwayDB`.
#'
#' @format A list of two pedigrees, named H1 and H2.
#'
#' @examples
#' pedtools::plotPedList(paternity, marker = "SE33")
#' markerSummary(paternity)
#'
#' forrel::kinshipLR(paternity)
"paternity"


#' Dataset for a full vs half sibship case
#'
#' A list of two pedigrees forming opposing hypotheses about two individuals
#' `NN1` and `NN2`: `FS` (full siblings) vs. `HS` (half siblings). Both
#' individuals are genotyped with the 23 markers included in the Fusion 6C kit.
#' Among the 23 markers, four pairs are linked:
#'
#' * TPOX and D2S441 (88.8 cM, 9 & 13 alleles)
#' * D5S818 and CSF1PO (27.8 cM, 9 & 11 alleles)
#' * vWA and D12S391 (11.9 cM, 12 & 23 alleles)
#' * D21S11 and Penta D (44.7 cM, 26 & 24 alleles)
#'
#' @format A list of two ped objects, named FS and HS.
#'
#' @examples
#' library(pedtools)
#' plotPedList(sibship, hatched = typedMembers)
#' markerSummary(sibship)
#' linkedLR(sibship)
"sibship"


#' Dataset for a case involving a putative half sibling.
#'
#' A list of two pedigrees forming opposing hypotheses about three individuals:
#'
#' * H1: A and B are full siblings, and C is their half brother
#' * H2: A and B are full siblings, and C is unrelated to them
#'
#' The individuals are typed with 50 markers, but some genotypes are missing.
#'
#' @format A list of two ped objects, named H1 and H2.
#'
#' @examples
#' library(pedtools)
#' plotPedList(halfsib, hatched = typedMembers)
#' markerSummary(halfsib)
#' linkedLR(halfsib)
"halfsib"