makeTransitionMatrix {GenABEL} | R Documentation |

## Genotype transition probabilities matrices...

### Description

Genotype transition probabilities matrices

### 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) |

### Details

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.)

### 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)

[Package

*GenABEL* version 1.6-7

Index]