R: Data for exercise in use of the snpStats package
for.exercise
R Documentation
Data for exercise in use of the snpStats package
Description
These data have been created artificially from publicly available
datasets. The SNPs have been selected from those genotyped by the
International HapMap Project
(http://www.hapmap.org)
to represent
the typical density found on a whole genome association chip, (the Affymetrix
500K platform,
http://www.affymetrix.com/support/technical/sample_data/500k_hapmap_genotype_data.affx
for a moderately sized chromosome (chromosome 10). A study of 500 cases and
500 controls has been simulated allowing for recombination using beta
software from Su and Marchini
(http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html).
Re-sampling of cases was weighted in such a
way as to simulate three “causal” locus on this chromosome, with
multiplicative effects of 1.3, 1.4 and 1.5 for each copy of the risk allele.
Usage
data(for.exercise)
Format
There are three data objects in the dataset:
snps.10:
An object of class "SnpMatrix"
containing a matrix of SNP genotype calls. Rows of the matrix
correspond to subjects and columns correspond to SNPs.
snp.support:
A conventional R
data frame containing information about the
SNPs typed (the chromosome position and the nucleotides
corresponding to the two alleles of the SNP).
subject.support:
A conventional R dataframe containing information about the study
subjects. There are two variables; cc gives case/control
status (1=case), and stratum gives ethnicity.
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(snpStats)
Loading required package: survival
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/snpStats/for.exercise.Rd_%03d_medium.png", width=480, height=480)
> ### Name: for.exercise
> ### Title: Data for exercise in use of the snpStats package
> ### Aliases: for.exercise snps.10 snp.support subject.support
> ### Keywords: datasets
>
> ### ** Examples
>
> data(for.exercise)
> snps.10
A SnpMatrix with 1000 rows and 28501 columns
Row names: jpt.869 ... ceu.464
Col names: rs7909677 ... rs12218790
> summary(snps.10)
$rows
Call.rate Certain.calls Heterozygosity
Min. :0.9879 Min. :1 Min. :0.0000
1st Qu.:0.9896 1st Qu.:1 1st Qu.:0.2993
Median :0.9900 Median :1 Median :0.3078
Mean :0.9900 Mean :1 Mean :0.3074
3rd Qu.:0.9904 3rd Qu.:1 3rd Qu.:0.3159
Max. :0.9919 Max. :1 Max. :0.3386
$cols
Calls Call.rate Certain.calls RAF MAF
Min. : 975 Min. :0.975 Min. :1 Min. :0.0000 Min. :0.0000
1st Qu.: 988 1st Qu.:0.988 1st Qu.:1 1st Qu.:0.2302 1st Qu.:0.1258
Median : 990 Median :0.990 Median :1 Median :0.5030 Median :0.2315
Mean : 990 Mean :0.990 Mean :1 Mean :0.5001 Mean :0.2424
3rd Qu.: 992 3rd Qu.:0.992 3rd Qu.:1 3rd Qu.:0.7671 3rd Qu.:0.3576
Max. :1000 Max. :1.000 Max. :1 Max. :1.0000 Max. :0.5000
P.AA P.AB P.BB z.HWE
Min. :0.00000 Min. :0.0000 Min. :0.00000 Min. :-21.9725
1st Qu.:0.06559 1st Qu.:0.2080 1st Qu.:0.06465 1st Qu.: -2.8499
Median :0.26876 Median :0.3198 Median :0.27492 Median : -1.1910
Mean :0.34617 Mean :0.3074 Mean :0.34647 Mean : -1.8610
3rd Qu.:0.60588 3rd Qu.:0.4219 3rd Qu.:0.60362 3rd Qu.: -0.1014
Max. :1.00000 Max. :0.5504 Max. :1.00000 Max. : 3.7085
NA's :4
> summary(snp.support)
chromosome position A1 A2
Min. :10 Min. : 101955 A:14019 C: 2349
1st Qu.:10 1st Qu.: 28981867 C:12166 G:12254
Median :10 Median : 67409719 G: 2316 T:13898
Mean :10 Mean : 66874497
3rd Qu.:10 3rd Qu.:101966491
Max. :10 Max. :135323432
> summary(subject.support)
cc stratum
Min. :0.0 CEU :494
1st Qu.:0.0 JPT+CHB:506
Median :0.5
Mean :0.5
3rd Qu.:1.0
Max. :1.0
>
>
>
>
>
> dev.off()
null device
1
>