Sib-pair Command: set impute

Class Data Declaration command
Name set impute
Arguments off | on | <level>

Toggles imputation routine.

Imputation level 0 (off) does not impute genotypes. It does generate legal genotypes for all untyped individuals for the MCMC IBD estimation. This approach is slowed by, and can fail (stochastically) in large pedigrees. In this case, the imputation level can be set to -1 (completely off!).
Imputation level 1 (on) imputes single individual's genotypes if unambiguous. All missing genotypes are silently imputed for the use of the MCMC IBD routine via sequential imputation and application of the Lange-Goradia algorithm. Imputation proceeds through the untyped founders, according to the collation order of the ID, then nonfounders according to the collation order of parental IDs.

Imputation level 2 makes the imputed values for the missing genotypes (in pedigrees where at least one member is typed at the locus) printable and writeable to files.

Example:

>> include volgaex.in
>> select pedigree AM
>> set impute off
>> write
 Writing  1  pedigrees:
!
!              S
!              e
!  Per Fat Mot x D14S52
!
AM 101 x   x   m   x/x
AM 102 x   x   f  83/87
AM 203 x   x   f  83/93
AM 201 101 102 m   x/x
AM 202 101 102 m   x/x
AM 204 101 102 m   x/x
AM 205 101 102 m  83/87
AM 206 101 102 m  83/87
AM 207 101 102 m   x/x
AM 208 101 102 m  83/87
AM 209 101 102 m  87/87
AM 210 101 102 m   x/x
AM 301 202 203 m  57/93

>> set impute 2
>> write
 Writing  1  pedigrees:
!
!              S
!              e
!  Per Fat Mot x D14S52
!
AM 101 x   x   m  57/87
AM 102 x   x   f  83/87
AM 203 x   x   f  83/93
AM 201 101 102 m  57/87
AM 202 101 102 m  57/87
AM 204 101 102 m  83/87
AM 205 101 102 m  83/87
AM 206 101 102 m  83/87
AM 207 101 102 m  57/83
AM 208 101 102 m  83/87
AM 209 101 102 m  87/87
AM 210 101 102 m  57/83
AM 301 202 203 m  57/93

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Class	Data Declaration command
Name	set impute
Arguments	off \| on \| <level>