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readme.renumf90 [2012/05/29 11:42] – ignacioreadme.renumf90 [2012/05/29 12:14] – [Fields in the parameter file] ignacio
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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> 
 TRAITS TRAITS
 t1 t2 .. tn t1 t2 .. tn
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 FIELDS_PASSED TO OUTPUT FIELDS_PASSED TO OUTPUT
 p1 p2 .. pm p1 p2 .. pm
-<file>+</file>
 fields p1-pn are passed to output without changes; can be empty fields p1-pn are passed to output without changes; can be empty
        
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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 +positions can be different for each trait for fixed effects;\\  
-effects; for random effects, only one position + 0 (misising) efefct are+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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 rtype is 'diagonal', 'sire' or 'animal' rtype is 'diagonal', 'sire' or '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  +current options include 
-permanent environment +  * 'pe' for permanent environment 
 +  * 'mat' for maternal 
 +  * 'mpe' for maternal permanent environment 
  
-<file>      +<file>
 FILE FILE
 fped fped
Line 117: Line 120:
 </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 +specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\ 
-alt_dam or yob can be replaced by 0; if this line is not given, defaults are  +missing alt_dam or yob can be replaced by 0\\ 
-1 2 3 0 0. If maternal effect is specified, the maternal effect is due to +if this line is not given, defaults are 1 2 3 0 0.\\ 
-position of d if alt_dam field is 0, or otherwise is due to alt_dam; If +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.
-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 +if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will 
-same format as fped and SNP info needs to start from a fixed column and +include the genomic information;\\ 
-include digits 0, 1, 2 and 5; ID and SNP info need to be separated by +file fsnp should start with ID with the same format as fped and SNP info needs to start from a fixed column and 
-at leats one space; see info for program PreGSf90  +include digits 0, 1, 2 and 5;\\ 
-<file>   +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
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 the default is 3; all pedigrees are loaded if p=0. the default is 3; all pedigrees are loaded if p=0.
  
-<file>    +<file>
 GEN_INT GEN_INT
 min avg max min avg max
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 pedigree. pedigree.
  
-<file>    +<file>
 REC_SEX REC_SEX
 i i
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 pedigree checks. pedigree checks.
  
-<file>    +<file>
 UPG_TYPE UPG_TYPE
 t t
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 custom_upg(year_of_birth,sex,ID, parent_code). custom_upg(year_of_birth,sex,ID, parent_code).
  
-<file>    +<file>
 RANDOM_REGRESSION  RANDOM_REGRESSION 
 r_type r_type
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 to be generated from a single data variable; not yet implemented to be generated from a single data variable; not yet implemented
  
-<file>    +<file>
 RR_POSITION RR_POSITION
 r1 .. rq r1 .. rq
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 </file> </file>
  
-<file>    +<file>
 (CO)VARIANCES (CO)VARIANCES
 g g
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 account for the maternal effect if present account for the maternal effect if present
  
-<file>    +<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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 //gmpe// are (co)variances for the MPE effect if present //gmpe// are (co)variances for the MPE effect if present
  
 +
 +----
  
 Sections starting from EFFECTS can be repeated any number of types. Sections starting from EFFECTS can be repeated any number of types.
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 skipped. Keywords out of order may not be recognized. skipped. Keywords out of order may not be recognized.
  
 +=====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: parameter used to read the input file:
  
  - the default size of character fields  - the default size of character fields
 +<file>
  OPTION alpha size nn  OPTION alpha size nn
 +</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 
 +<file>
  OPTION max_string_readline nn  OPTION max_string_readline nn
 +</file>
    where nn is the new size.    where nn is the new size.
  
  - the maximun number of fields    - the maximun number of fields  
 +<file>
         OPTION max_field_readline nn         OPTION max_field_readline nn
 +</file>
    where nn is the number of fields.     where nn is the number of fields. 
  
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-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. 
- COMBINE a b c ....+<file> 
 +COMBINE a b c .... 
 +</file>
 catenates b c ... into c. Keywords COMBINE need to be on top of the parameter catenates b c ... into c. Keywords COMBINE need to be on top of the parameter
 file, but possibly after comments. There may be many combined fields.  file, but possibly after comments. There may be many combined fields. 
 For example: For example:
- COMBINE 7 2 3 4+</file> 
 +COMBINE 7 2 3 4 
 +</file>
 combines content of fields 2 3 4 into field 7; the data file is not changed, 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).  only the program treats field 7 as fields 2 3 4 put together (without spaces). 
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-Additive Pedigree File +=====Additive Pedigree File======
-======================+
  
 The additive pedigree file(s) renadd* has the following structure: The additive pedigree file(s) renadd* has the following structure:
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-Extensions +=====Extensions=======
-==========+
  
 The program is being modified to support inbreeding, dominance, random The program is being modified to support inbreeding, dominance, random
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-Example +=====Example======
-========+
  
-data file - data.test + 
----------------------+**__data file__** - ''data.test'' 
 + 
 +<file>
 1 aa 34.5 11 12 zz 1 aa 34.5 11 12 zz
 3 bb 21.333 22 23 xx 3 bb 21.333 22 23 xx
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 3 aa  30 55 56 yy 3 aa  30 55 56 yy
 5 bb 1234567.890 66 67 zz 5 bb 1234567.890 66 67 zz
 +</file>
  
-pedigree file - test.ped + 
-------------------------+**__pedigree file__** - ''test.ped'' 
 +<file>
 qq 0 0 qq 0 0
 aa 0 0 aa 0 0
Line 311: Line 327:
 cc qq 0 cc qq 0
 dd 0 aa dd 0 aa
 +</file>
  
-parameter file - testpar1 + 
--------------------------+**__parameter file__** - ''testpar1'' 
 +<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 f programs.
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 RANDOM RANDOM
 diagonal diagonal
 +</file>
  
- +**__printout__** \\ 
-printout (temporary; the amount of details may change) +\\ 
-------------------------------------------------------+(temporary; the amount of details may change) 
 +<file>
  RENUMF90 version 1.93  RENUMF90 version 1.93
  name of parameter file? testpar1                                  name of parameter file? testpar1                                
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  Wrote parameter file "renf90.par"  Wrote parameter file "renf90.par"
  Wrote renumbered data "renf90.dat"  Wrote renumbered data "renf90.dat"
 +</file>
  
- +**__new parameter file__** - ''renf90.par'' 
-new parameter file - renf90.par +<file>
--------------------------------+
 # BLUPF90 parameter file created by RENF90 # BLUPF90 parameter file created by RENF90
 DATAFILE DATAFILE
Line 512: Line 532:
    1.000      0.1000        1.000      0.1000    
   0.1000       1.000   0.1000       1.000
 +</file>
  
  
  
-data file - renf90.dat +**__data file__** - ''renf90.dat'' 
-----------------------+<file>
  34.5 11 1 3 5 12 1 3 aa 1  34.5 11 1 3 5 12 1 3 aa 1
  21.333 22 2 1 3 23 2 1 bb 3  21.333 22 2 1 3 23 2 1 bb 3
Line 523: Line 544:
  30 55 2 3 5 56 2 2 aa 3  30 55 2 3 5 56 2 2 aa 3
  1234567.890 66 3 1 3 67 3 3 bb 5  1234567.890 66 3 1 3 67 3 3 bb 5
 +</file>
    
- Pedigree file (same format as from renum) - renadd02.ped + 
- --------------------------------------------------------+**__Pedigree file__** - ''renadd02.ped'' 
 +<file>
  1 6 3 1 0 2 2 0 0 bb  1 6 3 1 0 2 2 0 0 bb
  6 0 0 1 0 0 0 2 0 qq  6 0 0 1 0 0 0 2 0 qq
Line 534: Line 556:
  3 0 5 1 0 1 2 0 2 aa  3 0 5 1 0 1 2 0 2 aa
  4 6 7 1 0 2 1 0 0 cc  4 6 7 1 0 2 1 0 0 cc
 +</file>
  
-renumbering tables - renf90.tables +**''renumbering tables''** - ''renf90.tables'' 
-----------------------------------+<file>
  Effect group 1 of column 1 with 4 levels  Effect group 1 of column 1 with 4 levels
  Value    #    consecutive number  Value    #    consecutive number
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani
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