This dataset comprises several data frames from a fictional (and
unrealistically small) study. The
dataset started off as real data from a screen of non-synonymous SNPs
for association with type 1 diabetes, but the original identifiers have
been removed and a random case/control status has been generated.
Usage
data(testdata)
Format
There are five data objects in the dataset:
Autosomes: An object of class "SnpMatrix"
containing genotype calls for 400 subjects at 9445 autosomal SNPs
Xchromosome: An object of class "XSnpMatrix"
containing genotype calls for 400 subjects at 155 SNPs on the X
chromosome
Asnps: A dataframe containing information about the
autosomal SNPs. Here it contains only one variable,
chromosome, indicating the chromosomes on which the SNPs are
located
Xsnps: A dataframe containing information about the X
chromosome SNPs. Here it is empty and is only included for
completeness
subject.data: A dataframe containing information about
the subjects from whom each row of SNP data was obtained. Here it
contains:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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> library(snpStats)
Loading required package: survival
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/snpStats/testdata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: testdata
> ### Title: Test data for the snpStats package
> ### Aliases: testdata Autosomes Xchromosome Asnps Xsnps subject.data
> ### Keywords: datasets
>
> ### ** Examples
>
> data(testdata)
> Autosomes
A SnpMatrix with 400 rows and 9445 columns
Row names: 1987 ... 1473
Col names: 173760 ... 290959
> Xchromosome
An XSnpMatrix with 400 rows (214 haploid and 186 diploid), and 155 columns
Row names: 1987 ... 1473
Col names: 174193 ... 290917
> summary(Asnps)
rownames chromosome
173760 : 1 Min. : 1.000
173761 : 1 1st Qu.: 4.000
173762 : 1 Median : 9.000
173767 : 1 Mean : 9.373
173769 : 1 3rd Qu.:14.000
173770 : 1 Max. :22.000
(Other):9439
> summary(Xsnps)
rownames
174193 : 1
174196 : 1
174197 : 1
174208 : 1
174217 : 1
174219 : 1
(Other):149
> summary(subject.data)
rownames cc sex region
1 : 1 control:200 Male :214 Eastern :124
1002 : 1 case :200 Female:186 North-West : 66
1007 : 1 South-West : 55
1018 : 1 North Midlands: 48
1020 : 1 Midlands : 40
1022 : 1 E & W Ridings : 21
(Other):394 (Other) : 46
> summary(summary(Autosomes))
Length Class Mode
rows 18 table character
cols 63 table character
> summary(summary(Xchromosome))
Length Class Mode
sex 2 table numeric
rows 18 table character
cols 84 table character
>
>
>
>
>
> dev.off()
null device
1
>