Test data for family association tests

Description

These data started life as real data derived from an affected sibling pair study of type 1 diabetes. However, original subject and SNP identidiers have been replaced by randomly chosen ones.

Usage

data(families)

Format

There are two objects in the loaded data file:

• genotypes: An object of class "snp.matrix" containing the SNP genotype data for both parents and affected offspring

• pedData: A data frame containing the standard six fields for a LINKAGE pedfile. The are named familyid, member, father, mother sex, and affected

The two objects are linked by common row names.

Details

Coding in the pedData frame is as in the LINKAGE package, except that missing data are coded NA rather than zero

Examples

data(families)
summary(genotypes)
summary(pedData)

Results

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.
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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/families.Rd_%03d_medium.png", width=480, height=480)
> ### Name: families
> ### Title: Test data for family association tests
> ### Aliases: families genotypes pedData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(families)
> summary(genotypes)
$rows
   Call.rate      Certain.calls Heterozygosity  
 Min.   :0.6047   Min.   :1     Min.   :0.0000  
 1st Qu.:0.9535   1st Qu.:1     1st Qu.:0.2000  
 Median :0.9767   Median :1     Median :0.2558  
 Mean   :0.9535   Mean   :1     Mean   :0.2456  
 3rd Qu.:1.0000   3rd Qu.:1     3rd Qu.:0.3095  
 Max.   :1.0000   Max.   :1     Max.   :0.4524  

$cols
     Calls        Call.rate      Certain.calls      RAF          
 Min.   :2742   Min.   :0.9088   Min.   :1     Min.   :0.005711  
 1st Qu.:2842   1st Qu.:0.9418   1st Qu.:1     1st Qu.:0.046693  
 Median :2880   Median :0.9546   Median :1     Median :0.141840  
 Mean   :2877   Mean   :0.9535   Mean   :1     Mean   :0.168782  
 3rd Qu.:2906   3rd Qu.:0.9634   3rd Qu.:1     3rd Qu.:0.248441  
 Max.   :2964   Max.   :0.9824   Max.   :1     Max.   :0.453659  
      MAF                P.AA             P.AB              P.BB        
 Min.   :0.005711   Min.   :0.2951   Min.   :0.01142   Min.   :0.00000  
 1st Qu.:0.046693   1st Qu.:0.5659   1st Qu.:0.08774   1st Qu.:0.00295  
 Median :0.141840   Median :0.7358   Median :0.24479   Median :0.02132  
 Mean   :0.168782   Mean   :0.7077   Mean   :0.24700   Mean   :0.04528  
 3rd Qu.:0.248441   3rd Qu.:0.9096   3rd Qu.:0.37130   3rd Qu.:0.06486  
 Max.   :0.453659   Max.   :0.9886   Max.   :0.50779   Max.   :0.20244  
     z.HWE        
 Min.   :-1.9141  
 1st Qu.:-0.7872  
 Median :-0.1752  
 Mean   :-0.1078  
 3rd Qu.: 0.6820  
 Max.   : 2.0073  

> summary(pedData)
   familyid             member           father           mother      
 Length:3017        Min.   : 1.000   Min.   : 1.000   Min.   : 1.000  
 Class :character   1st Qu.: 2.000   1st Qu.: 1.000   1st Qu.: 1.000  
 Mode  :character   Median : 3.000   Median : 1.000   Median : 2.000  
                    Mean   : 2.789   Mean   : 1.496   Mean   : 1.679  
                    3rd Qu.: 4.000   3rd Qu.: 2.000   3rd Qu.: 2.000  
                    Max.   :18.000   Max.   :13.000   Max.   :10.000  
                                     NA's   :1485     NA's   :1485    
      sex           affected    
 Min.   :1.000   Min.   :1.000  
 1st Qu.:1.000   1st Qu.:1.000  
 Median :1.000   Median :2.000  
 Mean   :1.489   Mean   :1.521  
 3rd Qu.:2.000   3rd Qu.:2.000  
 Max.   :2.000   Max.   :2.000  
                 NA's   :1      
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>