GIMAP5.CEU | R Documentation |
SNP genotypes on HapMap founders from the CEU population for SNPs spanning the GIMAP5 gene.
data(GIMAP5.CEU)
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 "+") |
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).
International HapMap Project ftp://ftp.ncbi.nlm.nih.gov/hapmap/
The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320. 2005.
GIMAP5
require(snpStats) # for the SnpMatrix data structure data(GIMAP5.CEU) LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position)
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