GIMAP5

0th

Percentile

Example data set for LDHeatmap

SNP genotypes on HapMap founders for SNPs spanning the GIMAP5 gene.

Keywords
datasets
Usage
data(GIMAP5)
Details

SNP genotypes from HapMap release 27 for SNPs in a 10KB region spanning the GIMAP5 gene. Data are on founders from each of the 11 HapMap phase III populations:

ASW African ancestry in Southwest USA
CEU Utah residents with Northern and Western European ancestry from the CEPH collection
CHB Han Chinese in Beijing, China
CHD Chinese in Metropolitan Denver, Colorado
GIH Gujarati Indians in Houston, Texas
JPT Japanese in Tokyo, Japan
LWK Luhya in Webuye, Kenya
MEX Mexican ancestry in Los Angeles, California
MKK Maasai in Kinyawa, Kenya
TSI Toscani in Italia
YRI Yoruba in Ibadan, Nigeria

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).

Format

GIMAP5 is a list with three elements: snp.data, snp.support and subject.support. snp.data is a 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:

[,1] dbSNPalleles character alleles at each SNP
[,2] Assignment character same as dbSNPalleles
[,3] Chromosome character chromosome (chr7 for all)
[,4] Position numeric physical position
[,5] Strand character strand (all "+")

subject.support is a one-column data frame with:

[,1] pop character HapMap population of each subject

References

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

See Also

GIMAP5.CEU

Aliases
  • GIMAP5
Examples
# NOT RUN {
data(GIMAP5) 
#Now do a lattice plot with LDheatmaps in the panels
library(lattice)
pop<-GIMAP5$subject.support$pop
n<-nrow(GIMAP5$snp.data)
xyplot(1:n ~ 1:n | pop, type="n", scales=list(draw=FALSE), xlab="", ylab="",
      panel=function(x, y, subscripts,...) {
        LDheatmap(GIMAP5$snp.data[subscripts,],GIMAP5$snp.support$Position, 
                  newpage=FALSE)})
rm(pop,n)
# }
Documentation reproduced from package LDheatmap, version 0.99-7, License: GPL-3

Community examples

Looks like there are no examples yet.