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readme.renumf90 [2012/05/29 12:06] – ignacioreadme.renumf90 [2020/04/21 05:13] – 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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 The parameter file contains keywords in capital followed by specifications The parameter file contains keywords in capital followed by specifications
-of a given effect/data item. The keywords need to be typed exactly. Specific+of a given effect/data item.\\ The keywords need to be typed exactly.\\ Specific
 keywords need to occur sequentially, as shown below.  keywords need to occur sequentially, as shown below. 
  
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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> 
 +SKIP_HEADER 
 +n 
 +</file> 
 +This is optional. It skips the first n lines as header in the data file. 
 + 
 +<file>
 TRAITS TRAITS
 t1 t2 .. tn t1 t2 .. tn
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 w is  position of weight if present; can be empty w is  position of weight if present; can be empty
  
-<file>   +<file>
 RESIDUAL_VARIANCE RESIDUAL_VARIANCE
 r r
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 e1.. en type form e1.. en type form
 </file> </file>
-this line defines one group of effects; e1 .. en are positions of this  +this line defines one group of effects; e1 .. en are positions of this effect for all traits; 
-effect for all traits; positions can be different for each trait for fixed + 
-effects; for random effects, only one position + 0 (misising) efefct are+positions can be different for each trait for fixed effects; 
 + 
 +for random effects, only one position + 0 (misising) efefct are
 possible.  possible. 
   * type is 'cross' for crossclassified or 'cov' for covariables   * type is 'cross' for crossclassified or 'cov' for covariables
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 d1 .. dn form d1 .. dn form
 </file> </file>
-optional for covariables only, specifies nesting; form is as above+optional for covariables only, specifies nesting; 
 + 
 +form is as above
      
 <file> <file>
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 the RANDOM keyword occurs only if the current effect is random; the RANDOM keyword occurs only if the current effect is random;
-rtype is 'diagonal', 'sire' or 'animal'+rtype is: 
 +  * 'diagonal' 
 +  * 'sire'; not yet implemented 
 +  * 'animal'
  
-<file>   +<file>
 OPTIONAL OPTIONAL
 o1 o2.. oq o1 o2.. oq
 </file> </file>
-causes extra effects appended to the animal effect; current options include +causes extra effects appended to the animal effect;
-'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal  +
-permanent environment +
  
-<file>      +current options include: 
 +  * 'pe' for permanent environment 
 +  * 'mat' for maternal 
 +  * 'mpe' for maternal permanent environment; only if 'mat' is used 
 + 
 +<file>
 FILE FILE
 fped fped
 </file> </file>
  
-for animal and sire model only, fped specifies the pedigree file+for animal and sire model only 
 + 
 + //fped// specifies the pedigree file 
 + 
 +<file> 
 +SKIP_HEADER 
 +n 
 +</file> 
 +This is optional. It skips the first n lines as header in the pedigree file.
  
 <file> <file>
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 </file> </file>
  
-for animal effect only; specifies positions in the pedigree file of animal +for animal effect only; 
-an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob; missing + 
-alt_dam or yob can be replaced by 0; if this line is not given, defaults are  +specifies positions in the pedigree file of animal (an), sire (s), dam (d), alternate dam (alt_dam) , and year of birth (yob) 
-1 2 3 0 0. If maternal effect is specified, the maternal effect is due to + 
-position of d if alt_dam field is 0, or otherwise is due to alt_dam; If +missing alt_dam or yob can be replaced by 0 
-alt_dam field is not zero, it should include ID of real or recipient + 
-dam.+if this line is not given, defaults are 1 2 3 0 0. 
 + 
 +If maternal effect is specified, the maternal effect is due to position of d if alt_dam field is 0, or otherwise is due to alt_dam; 
 + 
 +If alt_dam field is not zero, it should include ID of real or recipient dam.
        
-<file>   +<file>
 SNP_FILE SNP_FILE
 fsnp fsnp
 </file> </file>
  
-optional; fsnp specifies files with ID and SNP information; if present, the  +optional;\\ 
-relationship matrix will be constructed as in Aguilar et al. (2010) and will +//fsnp// specifies files with ID and SNP information; 
-include the genomic information; file fsnp should start with ID with the + 
-same format as fped and SNP info needs to start from a fixed column and +if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will 
-include digits 0, 1, 2 and 5; ID and SNP info need to be separated by +include the genomic information; 
-at leats one space; see info for program PreGSf90  + 
-<file>   +file //fsnp// should start with ID with the same format as fped and SNP info needs to start from a fixed column and 
 +include digits 0, 1, 2 and 5; 
 + 
 + 
 +ID and SNP info need to be separated by at leats one space; see info for program [[readme.pregsf90|PreGSf90]]  
 + 
 +<file>
 PED_DEPTH PED_DEPTH
 p p
 </file> </file>
  
-optional for animal effect only; p specifies the depth of pedigree search;  +optional
-the default is 3; all pedigrees are loaded if p=0.+
  
-<file>    +for animal effect only; 
 + 
 +//p// specifies the depth of pedigree search; 
 + 
 +the default is 3 
 + 
 +all pedigrees are loaded if p=0. 
 + 
 +<file>
 GEN_INT GEN_INT
 min avg max min avg max
 </file> </file>
-optional; specifies minimum, average and maximum generation interval;+optional 
 + 
 +specifies minimum, average and maximum generation interval 
 applicable only if year of birth present; minimum and maximum used for applicable only if year of birth present; minimum and maximum used for
-pedigree checks; average used to predict year of birth of parent with missing+pedigree checks 
 + 
 +average used to predict year of birth of parent with missing
 pedigree. pedigree.
  
-<file>    +<file>
 REC_SEX REC_SEX
 i i
 </file> </file>
-optional; if only one sex has records, specifies which parent it is; used for +optional\\ 
-pedigree checks.+if only one sex has records, specifies which parent it is
  
-<file>    +used for pedigree checks. 
 + 
 +<file>
 UPG_TYPE UPG_TYPE
 t t
 </file> </file>
-optional;  +optional\\  
-if t is 'yob', the asignment is based on year of birth; the +  * if t is 'yob', the assignment is based on year of birth; the subsequent line should contain list of years to separate different UPG; 
-subsequent line should contain list of years to separate different UPG; +
        
-if t is 'in_pedigrees', the value of a missing parent should be -x, where x is +  * 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.
-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  +  * if t is 'internal',  allocation is by a user-written function custom_upg(year_of_birth,sex,ID, parent_code); not yet implemented.
-custom_upg(year_of_birth,sex,ID, parent_code).+
  
-<file>    +  * There are the other values for t: 'group', 'group_unisex', and 'group_sex'. See below for details. 
 + 
 +<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> 
 +It is the same as ''RANDOM_REGRESSION'' (see the explanation below) but it is effective only for fixed effects. 
 + 
 +<file>
 RANDOM_REGRESSION  RANDOM_REGRESSION 
 r_type r_type
 </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), this keyword also could be  +corresponding random effects (mat, pe and mpe) or the diagonal random effect.
-applied to set covariables for fixed effects; r_type is 'data' if covariables for +
-random regressions are in the data, or "legendre' if legendre plynomials are +
-to be generated from a single data variable; not yet implemented+
  
-<file>    +this keyword also could be applied to set covariables for fixed effects; 
 + 
 +//r_type// could be: 
 +  * 'data' if covariables for random regressions are in the data 
 +  * "legendre' if legendre plynomials are to be generated from a single data variable; not yet implemented 
 + 
 +<file>
 RR_POSITION RR_POSITION
 r1 .. rq r1 .. rq
 </file> </file>
-for random regressions, r1-rq specifies positions of covariables if +for random regressions,
-r_type='data', or r1 is order of legendre polynomial and r2 is position of +
-covariable if r_type='legendre'; not yet implemented +
-</file>+
  
-<file>    +  * //r1-rq// specifies positions of covariables if r_type='data' 
 +  * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type='legendre'; not yet implemented 
 + 
 +<file>
 (CO)VARIANCES (CO)VARIANCES
 g g
 </file> </file>
  
-//g// are (co)variances for the animal effect; the dimensions of g should  +//g// are (co)variances for the animal effect
-account for the maternal effect if present+
  
-<file>    +the dimensions of g should account for random correlated effect if present (maternal or random regression) 
 + 
 +<file>
 (CO)VARIANCES_PE (CO)VARIANCES_PE
 gpe gpe
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 //gpe// are (co)variances for the PE effect if present //gpe// are (co)variances for the PE effect if present
  
-<file> +<file>
 (CO)VARIANCES_MPE (CO)VARIANCES_MPE
 gmpe gmpe
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-----+==== User-defined UPG code ==== 
 + 
 +The program accepts one of the following keywords in ''UPG_TYPE'': ''group'', ''group_unisex'', and ''group_sex''. 
 +With one of these options, the program looks at a particular column in the pedigree file as a group code and use it for assigning the UPG code. If an animal has a missing parent, the program assigns an UPG code based on the group code. 
 + 
 +* ''group_unisex'': The program assign an UPG code to the unknown parent regardless of the parent's sex. 
 +* ''group'': The program assign a separate UPG code to the unknown sire and dam. 
 +* ''group_sex'': The user can specify a sex-specific UPG in the original pedigree file. 
 + 
 +For ''group_unisex'' and ''group'', 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 
 + 
 +For ''group_sex'', you need two additional columns in the pedigree file: one is for unknown sire and the other is for unknown dam. For example, assume the 5th column is for unknown sire and the 6th column is for unknown dam, the ''FILE_POS'' entry has 7 items. 
 + 
 +    FILE_POS 
 +    1 2 3 0 0 5 6 
 + 
 +The program now accept 3, 5, 6, or 7 items in ''FILE_POS''. 
 + 
 + 
 +=====Extra comments=====
  
 Sections starting from EFFECTS can be repeated any number of types. Sections starting from EFFECTS can be repeated any number of types.
 +
 If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0  If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 
 on diagonals and 0.1 on off-diagonals.  on diagonals and 0.1 on off-diagonals. 
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 The sequence of keywords should be as above although optional fields can be The sequence of keywords should be as above although optional fields can be
-skipped. Keywords out of order may not be recognized.+skipped. 
 + 
 +Keywords out of order may not be recognized.
  
-=====OPTIONS=====+=====Options=====
 The following options can added at the end of the parameter file to redefine The following options can added at the end of the parameter file to redefine
-parameter used to read the input file:+parameters used to read the input file:
  
- - the default size of character fields+ - the default size of character fields (default = 20)
 <file> <file>
- OPTION alpha size nn+OPTION alpha_size nn
 </file> </file>
-   where nn is the new size.+where //nn// is the new size.
  
- - the size of th record length + - the size of th record length (default = 800) 
 <file> <file>
- OPTION max_string_readline nn+OPTION max_string_readline nn
 </file> </file>
-   where nn is the new size.+where //nn// is the new size.
  
- - the maximun number of fields  + - the maximun number of fields (default = 100) 
 <file> <file>
-        OPTION max_field_readline nn+OPTION max_field_readline nn
 </file> </file>
-   where nn is the number of fields. +where //nn// is the number of fields. 
  
    
-The end of the parameter file for RENUMF90 can contain many lines beginning with OPTION.  +The end of the parameter file for ''RENUMF90'' can contain many lines beginning with OPTION.  
-All of these lines are passed to parameter file renf90.par to be used by  + 
-application programs. +All of these lines are passed to parameter file renf90.par to be used by application programs. 
  
  
 =====Combining fields or interactions====== =====Combining fields or interactions======
-Several fields in the data file can be combined into one using a COMBINE keyword. +Several fields in the data file can be combined into one using a ''COMBINE'' keyword. 
 <file> <file>
 COMBINE a b c .... COMBINE a b c ....
 </file> </file>
-catenates b c ... into c. Keywords COMBINE need to be on top of the parameter +catenates //b c// ... into //a//.\\ 
-file, but possibly after comments. There may be many combined fields. +Keyword COMBINE needs to be on top of the parameter file, but possibly after comments. 
 + 
 +There may be many combined fields. 
 For example: For example:
-</file>+<file>
 COMBINE 7 2 3 4 COMBINE 7 2 3 4
 </file> </file>
-combines content of fields 2 3 4 into field 7; the data file is not changed, + 
-only the program treats field 7 as fields 2 3 4 put together (without spaces).  +combines content of fields 2 3 4 into field 7; 
-The combined fields can be treated as "numeric", if they are composed of numbers + 
-and if their total length is <9. Otherwise, they need to be used as "alpha".  +the data file is not changed, only the program treats field 7 as fields 2 3 4 put together (without spaces). 
-Please note that the maximum size of the combined variable is limited by the + 
-largest size of the "alpha" field.  + 
 +The combined fields can be treated as "numeric", if they are composed of numbers and if their total length is <9. Otherwise, they need to be used as "alpha".\\ 
 + 
 +Please note that the maximum size of the combined variable is limited by the largest size of the "alpha" field.  
  
  
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    4) 3 minus number of known parents                                   4) 3 minus number of known parents                               
    5) known or estimated year of birth (0 if not provided)              5) known or estimated year of birth (0 if not provided)          
-   6) number of known parents (parents might be eliminated if not    +   6) number of known parents (parents might be eliminated if not contributing; 
-      contributing; 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)  +   8) number of progeny (before elimination due to other effects) as parent 1 
-      as parent 1 +   9) number of progeny (before elimination due to other effects) as parent 2  
-   9) number of progenies (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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