Example data set for LDheatmap

Description

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

Usage

data(GIMAP5.CEU)

Format

GIMAP5.CEU is a list with two elements: snp.data and snp.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:

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).

Source

International HapMap Project www.hapmap.org

References

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

See Also

GIMAP5

Examples

 
data(GIMAP5.CEU) 
LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position)

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/GIMAP5CEU.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GIMAP5.CEU
> ### Title: Example data set for LDheatmap
> ### Aliases: GIMAP5.CEU
> ### Keywords: datasets
> 
> ### ** Examples
>  
> data(GIMAP5.CEU) 
> LDheatmap(GIMAP5.CEU$snp.data,GIMAP5.CEU$snp.support$Position)
Loading required package: chopsticks
Loading required package: survival
Information: The input contains 116 samples with 23 snps
... Done
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>