Description Usage Format Source Examples
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.
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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.
The data were obtained from the diabetes and inflammation laboratory (see http://www-gene.cimr.cam.ac.uk)
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Loading required package: survival
Loading required package: Matrix
A SnpMatrix with 1000 rows and 28501 columns
Row names: jpt.869 ... ceu.464
Col names: rs7909677 ... rs12218790
$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
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
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
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