makeTransitionMatrix: Genotype transition probabilities matrices

In GenABEL: genome-wide SNP association analysis

Description

Function to generate genotypic transition probablilites matrices, which represent conditional probabilities P(g1|g2,nmeioses), where g1 is henotype of person one (AA, AB or BB), g2 is genotype of person two, and nmeioses is the number of meioses separating these two individuals (0 for twins, 1 for parent-offspring, c(2,2) for sibs, 2 for grandparent-grandchild pairs, etc.)

Usage

  makeTransitionMatrix(q, nmeioses = 1000)

Arguments

nmeioses	number of meioses separating two individuals ((a vector) of non-negative integers). If a vector, it is assumed it lists all meiotic paths connecting the pair
q	(a vector of) the coded allele frequency(ies) (e.g. "Q.2" of GenABEL-package)

Value

If q is scalar, a 3x3 matrix is returned, where elements represent conditional transition probabilities P(g1|g2,nmeioses); rows correspond to the genotypes of g1, and columns correspond to the genotypes of g2. If coded allele is 'B', then e.g. element [1,2] gives the probability P(g1='AA'|g2='AB',nmeioses=nmeioses).

If q is a vector, series of above-described matrices are returned as an 'array' object. A matrix constructed for certain element q[i] can be accessed via result[,,i].

Author(s)

Yurii Aulchenko

Examples

# transition matrix for parent-offspring, for q=0.1
makeTransitionMatrix(0.1,nmeioses=1)
# for a set of q's
makeTransitionMatrix(c(0.1,0.9),nmeioses=1)
# for sibs
makeTransitionMatrix(0.1,nmeioses=c(2,2))
# for half-sibs (or grandparent-grandchild)
makeTransitionMatrix(0.1,nmeioses=2)
# for remote relatives
makeTransitionMatrix(0.1,nmeioses=10)
# for independent
makeTransitionMatrix(0.1,nmeioses=1000)

Example output

Loading required package: MASS
Loading required package: GenABEL.data
     [,1] [,2] [,3]
[1,]  0.9 0.45  0.0
[2,]  0.1 0.50  0.9
[3,]  0.0 0.05  0.1
, , 1

     [,1] [,2] [,3]
[1,]  0.9 0.45  0.0
[2,]  0.1 0.50  0.9
[3,]  0.0 0.05  0.1

, , 2

     [,1] [,2] [,3]
[1,]  0.1 0.05  0.0
[2,]  0.9 0.50  0.1
[3,]  0.0 0.45  0.9

       [,1]   [,2]   [,3]
[1,] 0.9025 0.4275 0.2025
[2,] 0.0950 0.5450 0.4950
[3,] 0.0025 0.0275 0.3025
      [,1] [,2]  [,3]
[1,] 0.855 0.63 0.405
[2,] 0.140 0.34 0.540
[3,] 0.005 0.03 0.055
            [,1]       [,2]       [,3]
[1,] 0.810175781 0.80929688 0.80841797
[2,] 0.179843750 0.18062500 0.18140625
[3,] 0.009980469 0.01007813 0.01017578
     [,1] [,2] [,3]
[1,] 0.81 0.81 0.81
[2,] 0.18 0.18 0.18
[3,] 0.01 0.01 0.01

GenABEL documentation built on May 30, 2017, 3:36 a.m.