Genotype Data

Description

This is genotype data as read in by read.plink (snpStats). It contains genotypes for 99 individuals from the CEU population (Utah residents with northern and western European ancestry). It only includes chromosomes 13-15.

Usage

data("geno")

Format

The format is: List of 3 $ genotypes:Formal class 'SnpMatrix' [package "snpStats"] with 1 slot .. ..@ .Data: raw [1:99, 1:84195] 01 03 02 03 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:99] "CEU_1" "CEU_2" "CEU_3" "CEU_4" ... .. .. .. ..$ : chr [1:84195] "rs624673" "rs9511877" "rs638773" "rs9511880" ... $ fam :'data.frame': 99 obs. of 6 variables: ..$ pedigree: chr [1:99] "CEU_1" "CEU_2" "CEU_3" "CEU_4" ... ..$ member : int [1:99] 1 1 1 1 1 1 1 1 1 1 ... ..$ father : logi [1:99] NA NA NA NA NA NA ... ..$ mother : logi [1:99] NA NA NA NA NA NA ... ..$ sex : logi [1:99] NA NA NA NA NA NA ... ..$ affected: logi [1:99] NA NA NA NA NA NA ... $ map :'data.frame': 84195 obs. of 6 variables: ..$ chromosome: int [1:84195] 13 13 13 13 13 13 13 13 13 13 ... ..$ snp.name : chr [1:84195] "rs624673" "rs9511877" "rs638773" "rs9511880" ... ..$ cM : logi [1:84195] NA NA NA NA NA NA ... ..$ position : num [1:84195] 19743996 19744070 19744848 19745096 19745251 ... ..$ allele.1 : chr [1:84195] "G" "A" "A" "G" ... ..$ allele.2 : chr [1:84195] "A" "G" "G" "T" ...

Details

This data was filtered for: minor allele frequency < 0.01, call rate < 0.95, and Hardy-Weinberg Equilibrium p < 10^-6.

Source

ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/

References

The 1000 Genomes Project Consortium. (2012) <DOI:10.1038/nature11632> An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422), 56-65.

Examples

data("geno")

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(GenCAT)
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GenCAT/geno.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geno
> ### Title: Genotype Data
> ### Aliases: geno
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("geno")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>