AlgebraicHaploPackage-package: AlgebraicHaploPackage- The package haplotype a contingency of...

In AlgebraicHaploPackage: Haplotype Two Snips Out of a Paired Group of Patients

Description

Assume a group of patients of an unordered pair of data per snips. The contingency table of 2 snips on diffrent positions are calculated. A haplotype 2x2 most likely contingency table is guessed.

Details

Package:	AlgebraicHaploPackage
Type:	Package
Version:	1.2
Date:	2015-10-26
License:	GPL2.0

Author(s)

Jan Wolfertz.

Maintainer: [e-mail]

References

[1] 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. http://archpsyc.jamanetwork.com/article.aspx?articleid=210679. [2] Nathan Jacobson. Basic Algebra I: Second Edition (Dover Books on Mathematics). Dover Publication, 2009. [3] Montgomery Slatkin Laurent Excofie. Maximum-likelihood esti-mation of molecular haplotype frequencies in a diploid population. Molecular biology and evolution, 12(5):921 - 927, 1995. URL http://mbe.oxfordjournals.org/content/12/5/921.full.pdf. [4] Tianhua Niu. Algorithms for inferring haplotypes. Genetic Epidemiology, 27:334347, 2004. doi: DOI: 10.1002/gepi.20024. URL http://biostat.gru.edu/Journal [5] Werner A. Stahel. Statistische Datenanalyse Eine. Vieweg Verlag, 2002.

Examples

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)
### Check the result of the cubic equation of the second example
print("##############################")
print("Check the result of the cubic equation of the second example: \n")
temp2haplo =as.numeric(t(dd));
t2h=temp2haplo
haplotypeit(t2h[1],t2h[2],t2h[3],t2h[4],t2h[5],t2h[6],t2h[7],t2h[8],t2h[9]);
rm(temp2haplo)
rm(t2h)
### Third example
print("##############################")
print("Third example : \n")
dd3=matrix(c(1030,678,123,1,1,0,0,0,0),ncol=3,byrow=TRUE)
colnames(dd3)=c("AA","AG","GG")
rownames(dd3)=c("CC","CT","TT")
callhaplotype(dd3)
###  Check for alternative solutions
print("##############################")
print("Check for alternative solutions: \n")
temp2haplo =as.numeric(t(dd3));
t2h=temp2haplo;
haplotypeit(t2h[1],t2h[2],t2h[3],t2h[4],t2h[5],t2h[6],t2h[7],t2h[8],t2h[9]);
rm(temp2haplo)
rm(t2h)
print("##############################")
print("##############################")
print("This tests the result of the first example of the article \n")
dd2=matrix(c(4,0,0,0,30,0,0,0,23),ncol=3,byrow=TRUE)
callhaplotype(dd2)
callhaplotype(dd2)/(2*57)
print("##############################")

AlgebraicHaploPackage documentation built on May 2, 2019, 7:27 a.m.