Example of data set for LDHeatmap

CHBJPTSNP: Genotypes on 13 SNPs for 45 Chinese and 45 Japanese people CHBJPTDist: Physical map positions of the 13 SNPs

data(CHBJPTData)

Format

CHBJPTSNP: A dataframe of SNP genotypes. Each row represents an individual. Each column represents a SNP.

CHBJPTDist: a vector of integers, representing SNP physical map locations on the chromosome.

Source

International HapMap Project www.hapmap.org

Details

The data frame CHBJPTSNP contains genotypes for 13 SNPs on chromosome 7, from 45 Chinese and 45 Japanese individuals. The Chinese individuals were unrelated residents of the community at Beijing Normal University with at least 3 Han Chinese grandparents. The Japanese individuals were unrelated residents of the Tokyo metropolitan area with all grandparents from Japan. The data are from release 21 of the International HapMap project (The International HapMap Consortium 2005).

References

The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320. 2005.

Examples

 data(CHBJPTData)
#Now do our panel plot with LDheatmaps in the panels
library(lattice)
pop<-factor(c(rep("chinese", 45), rep("japanese", 45)))
xyplot(1:nrow(CHBJPTSNP) ~ 1:nrow(CHBJPTSNP) | pop, type="n",
      scales=list(draw=FALSE), xlab="", ylab="",
      panel=function(x, y, subscripts,...) {
        LDheatmap(CHBJPTSNP[subscripts,], CHBJPTDist, newpage=FALSE)})