R/GIMAP5CEUrd.R

In LDheatmap: Graphical Display of Pairwise Linkage Disequilibria Between SNPs

#' @name GIMAP5.CEU
#' @aliases GIMAP5.CEU
#' @docType data
#' @title Example data set for LDheatmap
#' @description SNP genotypes on HapMap founders from the CEU population
#'for SNPs spanning the GIMAP5 gene.
#' @usage data(GIMAP5.CEU)
#' @format GIMAP5.CEU is a list with two elements: snp.data and snp.support.
#'snp.data is a \code{SnpMatrix}
#'object containing the SNP genotypes. Rows correspond to
#'subjects and columns correspond to  SNPs.
#'snp.support is a data frame with the following columns:
#'\tabular{rlll}{
#'[,1] \tab dbSNPalleles   \tab character \tab alleles at each SNP\cr
#'[,2] \tab Assignment \tab character \tab same as dbSNPalleles\cr
#'[,3] \tab Chromosome   \tab character \tab chromosome (chr7 for all)\cr
#'[,4] \tab Position    \tab numeric \tab physical position\cr
#'[,5] \tab Strand   \tab character \tab strand (all "+")\cr
#'}
#' @details SNP genotypes from HapMap release 27
#'for SNPs in a 10KB region spanning
#'the GIMAP5 gene. Data are on founders from the CEU population,
#'described as Utah residents with Northern and Western European ancestry
#'from the CEPH collection.
#'Only those SNPs with minor allele frequency greater
#'than 5\% in all populations were retained.
#'The base positions are from NCBI build 36
#'(UCSC genome hg18).
#' @source International HapMap Project \url{ftp://ftp.ncbi.nlm.nih.gov/hapmap/}
#' @references The International HapMap Consortium. A haplotype map of
#'the human genome. Nature 437, 1299-1320. 2005.
#' @seealso \code{\link{GIMAP5}}
#' @examples require(snpStats) # for the SnpMatrix data structure
#'data(GIMAP5.CEU)
#'LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position)
#'
#' @keywords dataset
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