# Create an IBD matrix

### Description

Transform identity by descent (IBD) matrix data from the form produced by external programs such as SOLAR into the compact form used by the coxme and lmekin routines.

### Usage

1 | ```
ibdMatrix(id1, id2, x, idmap, diagonal)
``` |

### Arguments

`id1, id2` |
pairs of subject identifiers |

`x` |
the IBD value for that pair |

`idmap` |
an optional 2 column matrix or data frame whose first
element is the internal value (as found in |

`diagonal` |
optional value for the diagonal element. If present, any missing diagonal elements in the input data will be set to this value. |

### Details

The IBD matrix for a set of n subjects will be an n by n symmetric matrix whose i,j element is the contains, for some given genetic location, a 0/1 indicator of whether 0, 1/2 or 2/2 of the alleles for i and j are identical by descent. Fractional values occur if the IBD fraction must be imputed. The diagonal will be 1. Since a large fraction of the values will be zero, programs such as Solar return a data set containing only the non-zero elements. As well, Solar will have renumbered the subjects as 1:n in such a way that families are grouped together in the matrix; a separate index file contains the mapping between this new id and the original one. The final matrix should be labeled with the original identifiers.

### Value

a sparse matrix of class `dsCMatrix`

. This is the same form
used for kinship matrices.

### See Also

`kinship`

,
`Matrix`