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Last data update: 2014.03.03

R: Example data set for LDheatmap

GIMAP5

R Documentation

Example data set for LDheatmap

Description

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

Usage

data(GIMAP5)

Format

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

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).

Source

International HapMap Project www.hapmap.org

References

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

Examples

 
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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LDheatmap)
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LDheatmap/GIMAP5.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GIMAP5
> ### Title: Example data set for LDheatmap
> ### Aliases: GIMAP5
> ### Keywords: datasets
> 
> ### ** Examples
>  
> 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>