===== Fitting imprinting effects =====


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<code fortran>

!------------------------------------------------------------------------------
!                       Program GIN4IMPRINT
!                        
! Auxiliary program for WOMBAT to set up inverse of gametic relationship matrix
!
! Files written out allow imprinting effects to be fitted with a GIN covariance
! structure:
!   1. The .gin file -> default name: imprint.gin
!   2. The corresponding .codes file -> default name: imprint.codes
!      Gametes are coded as: animal ID * 10 + 1 (paternal) and 
!                            animal ID * 10 + 2 (maternal)
!                            => need to add corresponding column to data file!
! Input required:
!   Pedigree file (after pruning) with animal, sire and dam ID recoded in
!   running order and animals' inbreeding coefficients;
!   this can easily be generated by WOMBAT by running a set-up step for a
!   corresponding model without the imprinting effect(s) fitted
!
! Code for gametic relationship matrix written by Bruce Tier
!-------------------------------------------------------------km----02/2011-----


</code>

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WOMBAT readily allows for models fitting imprinting effects. These are best fitted as gametic effects, setting up the inverse of the gametic relationship matrix  externally and supplying it to the analysis  as ''.gin'' file.

 To make this task simpler, a FORTRAN program -- written by **Bruce Tier** -- is available:
   * Source code: [[wombat:gin4impf90|Gin4Imprint.f90]]
   * Source code & compiled executables (Linux and Windows 64-bit):  {{:wombat:gin4imprint.zip|Gin4Imprint.zip}} 

Details on its use are given as comments at the beginning of the source code and in the box on the right; an example analysis can be found in Example4/D. In brief:
  - Run the `Set-up' step in WOMBAT for a simple animal model, i.e. NOT fitting imprinting effects. This will generate the file: ''<nowiki>PrunedPedFile1.dat</nowiki>''\\ This file contains the pedigree information for animals in the analysis (after pruning), both as original codes and recoded from 1 to number of animals, together with their inbreeding coefficients.
  - Run ''<nowiki>Gin4Imprint</nowiki>''. This will use  the pedigree list and inbreeding coefficients from ''<nowiki>PrunedPedFile1.dat</nowiki>'' to:
    *  set up the inverse of the gametic relationship matrix and write it out in the format required by WOMBAT to be used as user-supplied covariance structure. The file containing this information has the default name ''imprint.gin''. Note that this matrix has twice the number of rows and columns than there are animals in the pedigree, corresponding to the two gametes for eacg individual.
    * write out a list of codes linking gamete effects to running numbers as file ''imprint.codes''\\ For each animal, the paternal gamete is coded as ID*10+1 where ID is the original animal code as supplied in data and pedigree files. Correspondingly, the maternal gamete is ID*10+2.\\ Note that this requires that for the largest ID, ID*10+2 does not exceed the biggest FORTRAN integer (2147483647; ''<nowiki>Gin4Imprint</nowiki>'' will stop with an error message if this occurs).
  - Add a column containing ID*10+i to your data file.\\ Use i=1 if you want to fit a paternal gamete and i=2 if you want to examine the effect of the maternal gamete; ''imprint.gin'' and ''imprint.codes'' are the same for both cases.
  - Update your parameter file by
    * calling this new column ''imprint'', 
    * adding ''RAN imprint GIN'' to the model block, and 
    * providing starting value(s) for the corresponding (co)variance components. 

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<code | imprint_example.par>
   PED pedigree.dat  
   DAT impdata.dat
     fixeff 2
     animal
     record
     imprint
   end
   ANAL UNI
   MODEL
     RAN animal NRM
     RAN imprint GIN
     FIX fixeff 
     TR record
   END
   VAR animal 1
   16
   VAR imprint 1
   2
   VAR error 1
   20
</code>
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Ready!

**N.B.** The above shows how to fit a gametic effect in addition to animals' additive genetic effects. Other models can be fitted analogously, e.g. we may wish to fit both maternal and paternal gametic effects and allow for a correlation between them, but exclude additive genetic effects.

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<code | bib>

@ARTICLE{cbruce11,
    author = {Tier, B. and Meyer, K.},
     title = {The effect of imprinted genes on carcass traits in Australian Angus and Hereford cattle},
   journal = {Proc. Ass. Advan. Anim. Breed. Genet.},
    volume = {19},
      year = {2011},
     pages = {63--66}
}

@article{tier2010,
  author =	 {Tier, B. and Meyer, K.},
  title =	 {On the analysis of parent-of-origin effects with
                  examples from ultrasonic measures of carcass traits
                  in Australian beef cattle},
  journal =	 {Journal of Animal Breeding and Genetics},
  year =	 2012,
  volume =	 129,
  number =	 5,
  pages =	 {359--368},
  url =		 {http://dx.doi.org/10.1111/j.1439-0388.2012.00996.x},
}

@Article{km11b,
  author =	 {Meyer, K. and Tier, B.},
  title =	 {Estimates of variances due to parent of origin
                  effects for weights of Australian beef cattle},
  journal =	 {Animal Production Science},
  year =	 2012,
  volume =	 {52},
  pages =	 {215--224},
  url =		 {http://dx.doi.org/10.1071/AN11195}
}

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