GIMAP5
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
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)
# }