# callhaplotype: calcultes the cotigency table of the haplotypes In AlgebraicHaploPackage: Haplotype Two Snips Out of a Paired Group of Patients

## Description

It starts with a contigency table of pairs of haplotypes and ends up with the haplotypes one. The heterocygote cases are the middle of the column and rows.

## Usage

 `1` ```callhaplotype(dd) ```

## Arguments

 `dd` This is a contingency table. Rows and columns are in the order are AA, AB,BB.

## Details

A 2x2 contingency table of haplotypes is calculated. The most likely solution had been choosen.

## Value

The haplotype contingency table is returned. All entries are numeric.

## Note

The differences are the coice of the solution of the cubic equations. About 4 percent differences and about 7 assuming 1 per thousand. For data export or import you can use a different package.

Jan Wolfertz

## References

David Clayton. "An r package for analysis of whole-genome association studies." Human Heredity, 64(1):45 - 51, 2007. doi: doi:10.1001/archgenpsychiatry.2010.25. URL http://archpsyc.jamanetwork.com/article.aspx?articleid=210679. Jan Wolfertz(in press.):""

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13``` ```print("###########################") dd2=matrix(c(4,0,0,0,30,0,0,0,23),ncol=3,byrow=TRUE) callhaplotype(dd2) callhaplotype(dd2)/(2*57) ### The second example print("##############################") print("The second example: \n") dd=matrix(c(1212, 2, 0, 679, 0,0,75,0,0), byrow=TRUE, nrow=3) colnames(dd)=c("CC","CT","TT") rownames(dd)=c("CC","CT","TT") callhaplotype(dd) print("##############################") ```

### Example output

```[1] "###########################"
[,1] [,2]
[1,]   38    0
[2,]    0   76
[,1]      [,2]
[1,] 0.3333333 0.0000000
[2,] 0.0000000 0.6666667
[1] "##############################"
[1] "The second example: \n"
[,1] [,2]
[1,] 3105  829
[2,]    2    0
[1] "##############################"
```

AlgebraicHaploPackage documentation built on May 29, 2017, 9:12 p.m.