GIMAP5.CEU

0th

Percentile

Example data set for LDheatmap

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

Keywords
dataset
Usage
data(GIMAP5.CEU)
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).

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 "+")

References

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

See Also

GIMAP5

Aliases
  • GIMAP5.CEU
Examples
# NOT RUN {
require(snpStats) # for the SnpMatrix data structure
data(GIMAP5.CEU)
LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position)

# }
Documentation reproduced from package LDheatmap, version 0.99-7, License: GPL-3

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