AlgebraicHaploPackage (version 1.2)

haplotypeit: Haplotype a 3 x 3 counting matrix.

Description

This functions recalculates the potential 2x2 haplotype matrics. It gets a 3x3 matrixs and returns a list A,B,C,D of vectors. A[1],B[1],C[1],D[1] is the first solution of the matrix. There are always three solutions.

Usage

haplotypeit(a, b, c, d, e, f, g, h, i)

Arguments

a

Number of counts of matching snip pairs.

b

Number of counts of matching snip pairs..

c

Number of counts of matching snip pairs.

d

Number of counts of matching snip pairs.

e

Number of counts of matching snip pairs.

f

Number of counts of matching snip pairs.

g

Number of counts of matching snip pairs.

h

Number of counts of matching snip pairs.

i

Number of counts of matching snip pairs.

Value

output$A is a vector of length 3. output$B,Output$C, output$D is eighter of length 3. One potential solution is A[1],B[1],C[1],D[1].

Details

The software automatically resolves the cases e=0 by circumventing the cubic equation. If the degree of the equation is lower additional copies of some solution will be made to produce the outputformat. The output format is a list of four vectors of copefficients. Each vector contains three complex numbers.

References

This methods refers to an article: 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.

See Also

callhaplotype

Examples

haplotypeit(4,0,0,0,30,0,0,0,23)
print("##############################")
print("This tests the cubic routine")
haplotypeit(4,0,0,0,30,0,0,0,23)
### Formated of 4 digits
print("Formated of 4 digits")
round(as.numeric(Re(haplotypeit(4,0,0,0,30,0,0,0,23)$A)),digit=4)
round(as.numeric(Re(haplotypeit(4,0,0,0,30,0,0,0,23)$B)),digit=4)
round(as.numeric(Re(haplotypeit(4,0,0,0,30,0,0,0,23)$C)),digit=4)
round(as.numeric(Re(haplotypeit(4,0,0,0,30,0,0,0,23)$D)),digit=4)
###