\begin{Schunk}
\begin{Sinput}
> library(ceu1kg)
> data(ceu1KG.sml)
\end{Sinput}
\end{Schunk}
\begin{Schunk}
\begin{Sinput}
> sapply(ceu1KG.sml, dim)
\end{Sinput}
\begin{Soutput}
       chr1   chr2   chr3   chr4   chr5   chr6   chr7   chr8   chr9  chr10
[1,]     60     60     60     60     60     60     60     60     60     60
[2,] 605756 664326 556362 567547 499164 518645 451004 429055 328069 396487
      chr11  chr12  chr13  chr14  chr15  chr16  chr17  chr18  chr19  chr20
[1,]     60     60     60     60     60     60     60     60     60     60
[2,] 381826 365883 293253 254837 210540 238117 196327 225279 157182 174484
      chr21  chr22
[1,]     60     60
[2,] 109143 101568
\end{Soutput}
\end{Schunk}
{\huge
\bi
\item derived from the VCF representation of all calls for CEU
\item distributed as a 700MB gzipped tabix-indexed file
\item \texttt{GGtools:::vcf2sm} imports record-at-a-time
decompressing on the fly
\ei
}

\clearpage

\begin{Schunk}
\begin{Sinput}
> ceu1KG.sml[[1]][1:2, 1:5]
\end{Sinput}
\begin{Soutput}
A snp.matrix with  2 rows and  5 columns
Row names:  NA06985 ... NA06986 
Col names:  chr1:533 ... rs2462492 
\end{Soutput}
\begin{Sinput}
> as(ceu1KG.sml[[1]][1:2, 1:5], "matrix")
\end{Sinput}
\begin{Soutput}
        chr1:533 chr1:41342 chr1:41791 chr1:44449 rs2462492
NA06985       01         01         01         01        01
NA06986       01         02         01         01        01
\end{Soutput}
\begin{Sinput}
> as(ceu1KG.sml[[1]][1:2, 1:5], "character")
\end{Sinput}
\begin{Soutput}
        chr1:533 chr1:41342 chr1:41791 chr1:44449 rs2462492
NA06985 "A/A"    "A/A"      "A/A"      "A/A"      "A/A"    
NA06986 "A/A"    "A/B"      "A/A"      "A/A"      "A/A"    
\end{Soutput}
\end{Schunk}

\clearpage

\begin{Schunk}
\begin{Sinput}
> ceu1kg
\end{Sinput}
\begin{Soutput}
snp.matrix-based genotype set:
number of samples:  41 
number of chromosomes present:  22 
annotation: illuminaHumanv1.db 
Expression data dims: 47293 x 41 
Phenodata: An object of class "AnnotatedDataFrame"
  sampleNames: NA06985, NA06994, ..., NA12874  (41 total)
  varLabels and varMetadata description:
    famid: hapmap family id
    persid: hapmap person id
    ...: ...
    male: logical TRUE if male
    (7 total)
\end{Soutput}
\begin{Sinput}
> dim(exprs(ceu1kg))
\end{Sinput}
\begin{Soutput}
[1] 47293    41
\end{Soutput}
\end{Schunk}

\clearpage

\begin{Schunk}
\begin{Sinput}
> summary(smList(ceu1kg)[[20]])
\end{Sinput}
{\Large
\begin{Soutput}
$rows
   Call.rate Heterozygosity  
 Min.   :1   Min.   :0.2114  
 1st Qu.:1   1st Qu.:0.2285  
 Median :1   Median :0.2339  
 Mean   :1   Mean   :0.2358  
 3rd Qu.:1   3rd Qu.:0.2430  
 Max.   :1   Max.   :0.2555  

$cols
     Calls      Call.rate      MAF               P.AA             P.AB        
 Min.   :41   Min.   :1   Min.   :0.00000   Min.   :0.0000   Min.   :0.00000  
 1st Qu.:41   1st Qu.:1   1st Qu.:0.03659   1st Qu.:0.3659   1st Qu.:0.07317  
 Median :41   Median :1   Median :0.12195   Median :0.7317   Median :0.19512  
 Mean   :41   Mean   :1   Mean   :0.16550   Mean   :0.6361   Mean   :0.23579  
 3rd Qu.:41   3rd Qu.:1   3rd Qu.:0.28049   3rd Qu.:0.9268   3rd Qu.:0.39024  
 Max.   :41   Max.   :1   Max.   :0.50000   Max.   :1.0000   Max.   :0.92683  
                                                                              
      P.BB             z.HWE  (8173 NA)
 Min.   :0.00000   Min.   :  -6.4031  
 1st Qu.:0.00000   1st Qu.:  -0.1525  
 Median :0.02439   Median :   0.1746  
 Mean   :0.12815   Mean   :   0.0892  
 3rd Qu.:0.14634   3rd Qu.:   0.5578  
 Max.   :1.00000   Max.   :   5.4731  
\end{Soutput}
}
\end{Schunk}

