testdata: Test data for the snpMatrix package

In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

Description

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:

• AutosomesAn object of class "snp.matrix" containing genotype calls for 400 subjects at 9445 autosomal SNPs

• XchromosomeAn object of class "X.snp.matrix" containing genotype calls for 400 subjects at 155 SNPs on the X chromosome

• AsnpsA dataframe containing information about the autosomal SNPs. Here it contains only one variable, chromosome, indicating the chromosomes on which the SNPs are located

• XsnpsA dataframe containing information about the X chromosome SNPs. Here it is empty and is only included for completeness

• subject.dataA dataframe containing information about the subjects from whom each row of SNP data was obtained. Here it contains:

  • ccCase-control status

  • sexSex

  • regionGeographical region of residence

Source

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

References

http://www-gene.cimr.cam.ac.uk/clayton

Examples

data(testdata)
Autosomes
Xchromosome
summary(Asnps)
summary(Xsnps)
summary(subject.data)
summary(summary(Autosomes))
summary(summary(Xchromosome))

Example output

A snp.matrix with  400 rows and  9445 columns
Row names:  1987 ... 1473 
Col names:  173760 ... 290959 
An X.snp.matrix with  400 rows and  155 columns, 
holding data for 214  males and  186  females
Row names:  1987 ... 1473 
Col names:  174193 ... 290917 
    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                   
    rownames  
 174193 :  1  
 174196 :  1  
 174197 :  1  
 174208 :  1  
 174217 :  1  
 174219 :  1  
 (Other):149  
    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  
     Calls         Call.rate           MAF              P.AA        
 Min.   :  0.0   Min.   :0.0000   Min.   :0.0000   Min.   :0.00000  
 1st Qu.:265.0   1st Qu.:0.6625   1st Qu.:0.0325   1st Qu.:0.03275  
 Median :394.0   Median :0.9850   Median :0.1713   Median :0.26984  
 Mean   :346.3   Mean   :0.8657   Mean   :0.1920   Mean   :0.38189  
 3rd Qu.:398.0   3rd Qu.:0.9950   3rd Qu.:0.3289   3rd Qu.:0.70551  
 Max.   :400.0   Max.   :1.0000   Max.   :0.5000   Max.   :1.00000  
                                  NA's   :43       NA's   :43       
      P.AB              P.BB             z.HWE         
 Min.   :0.00000   Min.   :0.00000   Min.   :-19.9499  
 1st Qu.:0.06172   1st Qu.:0.02506   1st Qu.: -0.5980  
 Median :0.28444   Median :0.22822   Median :  0.0754  
 Mean   :0.25975   Mean   :0.35836   Mean   : -0.0197  
 3rd Qu.:0.43609   3rd Qu.:0.66582   3rd Qu.:  0.6803  
 Max.   :1.00000   Max.   :1.00000   Max.   : 16.2481  
 NA's   :43        NA's   :43        NA's   :1254      
     Calls         Call.rate           MAF                P.AA        
 Min.   :  0.0   Min.   :0.0000   Min.   :0.000000   Min.   :0.00000  
 1st Qu.:264.0   1st Qu.:0.6600   1st Qu.:0.007812   1st Qu.:0.03226  
 Median :389.0   Median :0.9725   Median :0.113990   Median :0.30811  
 Mean   :333.8   Mean   :0.8345   Mean   :0.174095   Mean   :0.42316  
 3rd Qu.:397.0   3rd Qu.:0.9925   3rd Qu.:0.313218   3rd Qu.:0.83607  
 Max.   :400.0   Max.   :1.0000   Max.   :0.496552   Max.   :1.00000  
                                  NA's   :2          NA's   :2        
      P.AB              P.BB               P.AY             P.BY        
 Min.   :0.00000   Min.   :0.000000   Min.   :0.0000   Min.   :0.00000  
 1st Qu.:0.01081   1st Qu.:0.005405   1st Qu.:0.1619   1st Qu.:0.07729  
 Median :0.18852   Median :0.195652   Median :0.5461   Median :0.45390  
 Mean   :0.23098   Mean   :0.345855   Mean   :0.5430   Mean   :0.45699  
 3rd Qu.:0.43784   3rd Qu.:0.655462   3rd Qu.:0.9227   3rd Qu.:0.83810  
 Max.   :0.72283   Max.   :1.000000   Max.   :1.0000   Max.   :1.00000  
 NA's   :2         NA's   :2          NA's   :2        NA's   :2        
     z.HWE           Calls.female  
 Min.   :-3.60226   Min.   :  0.0  
 1st Qu.:-0.55347   1st Qu.:122.0  
 Median : 0.13749   Median :184.0  
 Mean   : 0.06628   Mean   :157.5  
 3rd Qu.: 0.51360   3rd Qu.:186.0  
 Max.   : 7.67702   Max.   :186.0  
 NA's   :36                        

chopsticks documentation built on Nov. 8, 2020, 7:51 p.m.