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readme.renumf90 [2012/05/29 12:37] – [Additive Pedigree File] ignacioreadme.renumf90 [2018/05/18 23:35] – yutaka
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 =======RENUMF90====== =======RENUMF90======
-renumbering program for the BLUPF90 family now works with SNP info\\+A renumbering program for the ''BLUPF90'' family now works with SNP info\\
 Ignacy Misztal and Ignacio Aguilar, University of Georgia\\ Ignacy Misztal and Ignacio Aguilar, University of Georgia\\
 August 27, 2001 - Mar 17, 2011 August 27, 2001 - Mar 17, 2011
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 Lines with # are treated as comments Lines with # are treated as comments
              
-<file> +<file>
 DATAFILE DATAFILE
 f1 f1
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 The data file is f1 The data file is f1
  
-<file> +<file>
 TRAITS TRAITS
 t1 t2 .. tn t1 t2 .. tn
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 rtype is: rtype is:
   * 'diagonal'   * 'diagonal'
-  * 'sire'+  * 'sire'; not yet implemented
   * 'animal'   * 'animal'
  
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   * 'pe' for permanent environment   * 'pe' for permanent environment
   * 'mat' for maternal   * 'mat' for maternal
-  * 'mpe' for maternal permanent environment +  * 'mpe' for maternal permanent environment; only if 'mat' is used
  
 <file> <file>
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 for animal effect only; for animal effect only;
  
-specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\+specifies positions in the pedigree file of animal (an), sire (s), dam (d), alternate dam (alt_dam) , and year of birth (yob) 
 missing alt_dam or yob can be replaced by 0 missing alt_dam or yob can be replaced by 0
  
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   * if t is 'in_pedigrees', the value of a missing parent should be -x, where x is UPG number that this missing parent should be allocated to; in this option, all known parents should have pedigree lines, i.e., each parent field should contain either the ID of a real parent, or a negative UPG number.   * if t is 'in_pedigrees', the value of a missing parent should be -x, where x is UPG number that this missing parent should be allocated to; in this option, all known parents should have pedigree lines, i.e., each parent field should contain either the ID of a real parent, or a negative UPG number.
        
-  * if t is 'internal',  allocation is by a user-written function custom_upg(year_of_birth,sex,ID, parent_code).+  * if t is 'internal',  allocation is by a user-written function custom_upg(year_of_birth,sex,ID, parent_code); not yet implemented. 
 +<file> 
 +INBREEDING 
 +inb_type 
 +</file> 
 +optional\\ 
 +use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file 
 + 
 +//inb_type// could be: 
 +  * 'pedigree' - the program computes inbreeding coefficients with Meuwissen and Luo (1992) using the pedigree to be saved in renaddxx.ped; calculated inbreeding coefficients will be saved in a file "renf90.inb" with the original ID 
 +  * 'file' - the program reads inbreeding coefficients from an external file. You should put the filename after 'file' e.g. 'file inbreeding.txt'. The file has at least 2 columns: original_ID and inbreeding value (from 0.0 to 1.0). The program just skips unnecessary IDs 
 + 
 +<file> 
 +FIXED_REGRESSION  
 +r_type 
 +</file> 
 +The same feature as ''RANDOM_REGRESSION'' (see the explanation below) but it is effective only for fixed effects.
  
 <file> <file>
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 </file> </file>
 Specifies that random regressions should be applied to the animal and Specifies that random regressions should be applied to the animal and
-corresponding effects (mat, pe and mpe)+corresponding random effects (mat, pe and mpe) or the diagonal random effect.
  
 this keyword also could be applied to set covariables for fixed effects; this keyword also could be applied to set covariables for fixed effects;
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 </file>  </file> 
 //gmpe// are (co)variances for the MPE effect if present //gmpe// are (co)variances for the MPE effect if present
 +
 +
 +==== User-defined UPG code ====
 +
 +The program accepts the following keywords in ''UPG_TYPE''.
 +
 +    UPG_TYPE
 +    group
 +    
 +    or
 +    
 +    UPG_TYPE
 +    group_unisex
 +
 +With this option, the program looks at a particular column in the pedigree file as a group code and saves it. If an animal has a missing parent, the program assigns an UPG code according to the group code. If you want to assign separate UPGs by the parent's sex (sire or dam), use ''group''. The ''group_unisex'' doesn't consider the sex of parents.
 +
 +The column in the pedigree file is specified with the 6th item in ''FILE_POS''. The following example tells the program the 5th column in the pedigree file as the group code. The group code will be treated as characters.
 +
 +    FILE_POS
 +    1 2 3 0 0 5
 +
 +The program now accept 3 items, 5 items, or 6 items in ''FILE_POS''.
 +
  
  
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  - the default size of character fields  - the default size of character fields
 <file> <file>
-OPTION alpha size nn+OPTION alpha_size nn
 </file> </file>
 where //nn// is the new size. where //nn// is the new size.
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 </file> </file>
 catenates //b c// ... into //a//.\\ catenates //b c// ... into //a//.\\
-Keywords COMBINE need to be on top of the parameter file, but possibly after comments.+Keyword COMBINE needs to be on top of the parameter file, but possibly after comments.
  
 There may be many combined fields.  There may be many combined fields. 
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       if animal has genotype 10+number of know parents                                                         if animal has genotype 10+number of know parents                                                  
    7) number of records                 7) number of records             
-   8) number of progenies (before elimination due to other effects) as parent 1 +   8) number of progeny (before elimination due to other effects) as parent 1 
-   9) number of progenies (before elimination due to other effects) as parent 2  +   9) number of progeny (before elimination due to other effects) as parent 2  
   10) original animal id                                               10) original animal id                                            
  
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 <file> <file>
 # Parameter file for program renf90; it is translated to parameter # Parameter file for program renf90; it is translated to parameter
-# file for BLUPF90 family f programs.+# file for BLUPF90 family programs.
 DATAFILE DATAFILE
 data.test data.test
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani
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