Example data set for LDheatmap

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

data(GIMAP5.CEU)

Format

GIMAP5.CEU is a list with two elements: snp.data and snp.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 "+")
	[,1]	dbSNPalleles	character

Source

International HapMap Project www.hapmap.org

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).

References

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

See also

GIMAP5

Examples

require(snpStats) # for the SnpMatrix data structure
#> Loading required package: snpStats
#> Loading required package: survival
#> Warning: package ‘survival’ was built under R version 3.4.4
#> Loading required package: Matrix
#> Warning: package ‘Matrix’ was built under R version 3.4.4
data(GIMAP5.CEU)
LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position)