R/datasets.R

In paramlink: Parametric Linkage and Other Pedigree Analysis in R

#' Example pedigree for linkage analysis
#'
#' Medical pedigree with 23 individuals of which 15 are genotyped with 650 SNP
#' markers. Eleven family members are affected by a disease, showing an
#' autosomal dominant inheritance pattern.
#'
#' @docType data
#' @format A data frame with 23 rows and 1306 columns, describing the pedigree and
#' marker data in pre-makeped format. The first 6 columns contain the pedigree
#' structure and affection status, while the final 1300 columns hold the marker alleles.
#' \itemize{
#'   \item FAMID. Family ID
#'   \item ID. Individual ID
#'   \item FID. Father ID
#'   \item MID. Mother ID
#'   \item SEX. Gender (male=1, female=2)
#'   \item AFF. Affection status (unaffected=1, affected=2, unknown=0)
#'   \item M1_1. First allele of marker 1
#'   \item M1_2. Second allele of marker 1
#'   \item ...
#'   \item M650_1. First allele of marker 650
#'   \item M650_2. Second allele of marker 650
#' }
#' All markers are SNPs, whose alleles are written as 1 and 2.
#' Missing alleles are denoted by 0.
#'
#' @examples
#'
#' x = linkdat(dominant)
#' summary(x)
#'
"dominant"


#' Toy pedigree for linkage analysis
#'
#' Toy pedigree with 4 individuals typed at a single SNP marker. Individual 1 is
#' missing one allele.
#'
#' The format is standard LINKAGE (pre-makeped) format, with columns as follows:
#' \itemize{
#'   \item FAMID. Family ID
#'   \item ID. Individual ID
#'   \item FID. Father ID
#'   \item MID. Mother ID
#'   \item SEX. Gender (male=1, female=2)
#'   \item AFF. Affection status (unaffected=1, affected=2, unknown=0)
#'   \item M_A1. First allele of marker 1
#'   \item M_A2. Second allele of marker 1
#' }
#' @docType data
#'
#' @format A data frame with 4 rows and 8 columns
#'
#' @examples
#'
#' toyped
#' linkdat(toyped)
#'
"toyped"


#' A consanguineous pedigree
#'
#' A consanguineous pedigree with two inbreeding loops.
#'
#'
#' @docType data
#'
#' @format A data frame with 17 rows and 6 columns.
#' See \code{\link{toyped}} for details about the format.
#'
#' @examples
#'
#' x = linkdat(twoloops)
#' plot(x)
#'
"twoloops"


#' Example pedigree with X-linked disease pattern.
#'
#' A complex pedigree with an X-linked recessive disease pattern
#'
#' The format is standard LINKAGE (pre-makeped) format.
#'
#' @name Xped
#' @docType data
#'
#' @format A data frame with 15 rows and 6 columns. See \code{\link{toyped}} for
#'   details about the format.
#'
#' @examples
#'
#' Xped
#'
#' # Convert to a 'linkdat' object and set a recessive X-linked model:
#' x = linkdat(Xped, model=4)
#' summary(x)
"Xped"