for.exercise: Data for exercise in use of the snpStats package

In snpStats: SnpMatrix and XSnpMatrix classes and methods

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.

Source

The data were obtained from the diabetes and inflammation laboratory (see http://www-gene.cimr.cam.ac.uk)

Examples

data(for.exercise)
snps.10
summary(snps.10)
summary(snp.support)
summary(subject.support)

Example output

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                

snpStats documentation built on Nov. 8, 2020, 10:59 p.m.