Parameter file elements

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<pedigrees>

<root>
 ..
 <pedigrees>
  pedigrees: a,b
  ...
 </pedigrees>
</root>
example host element element type purpose

content:

  • key strings
word example type variable type variable values default explanation
pedigrees pedigrees: a,b compulsory csv word-list pedigree names none
  • nominated-compulsory elements

<pedigree name>

<root>
 ..
 <pedigrees>
  pedigrees: myped
  ..
  <myped>
   file: myped.csv
   switch: selfing
   phantomparents: 2
  </myped>
  ..
 </pedigrees>
</root>
example host element element type purpose

content:

  • key strings
word example type variable type variable values default explanation
file file: myped.csv compulsory word file name none list content determines the name of the file containing the pedigree
switch switch: selfing optional csv-word-list selfing,probabilistic none list content determines pedigree properties.
  • selfing: both parents can have the same id
  • probabilistic: each individual can have more than 1 pair of parents
phantomparents phantomparents: 2 optional single numeric value positive integer none integer number determines the number of individuals at the top of the pedigree which are phantom parents

<genotypes>

Example host type purpose 
<root>
 ..
 <genotypes>
  genotypes: a,b
  ...
 </genotypes>
</root>
 root automatic-optional hosts one to several elements each containing information about different sets of genotypes

content:

  • key strings
word example type variable type variable values default explanation
genotypes genotypes: a,b compulsory csv word-list genotype names none list content determines names of nominated-compulsory elements
  • nominated-compulsory elements

<genotype name>

Example host type purpose 
<root>
 ..
 <genotypes>
  genotypes: mygn
  ..
  <mygn>
   file: genotypes.txt
   pedigree: myped
   cross: crossref.csv
  </mygn>
  ..
 </genotypes>
</root>
 genotypes nominated-compulsory hosts information about a specific set of genotypes identified by genotype name

content:

  • key strings
word example type variable type variable values default explanation
file file: genotype.txt compulsory word file name none content determines the name of the file containing the genotypes
cross cross: mycross.csv optional word file name none content determines the name of the file containing the pedigree ids related to the genotypes
pedigree pedigree: myped optional word pedigree name none content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file

<grms>

Example host type purpose 
<root>
 ..
 <grms>
  grms: a,b
  ...
 </grms>
</root>
 root automatic-optional hosts one to several elements each containing information about a specific grm

content:

  • key strings
word example type variable type variable values default explanation
grms grms: x,y compulsory csv word-list grm names none list content determines names of nominated-compulsory elements
  • nominated-compulsory elements

<grm name>

Example host type purpose 
<root>
 ..
 <grms>
  grms: mygrm
  ..
  <mygrm>
   genotype: mygn
   method: YA
  </mygrm>
  ..
 </genotypes>
</root>
 grms nominated-compulsory hosts information about a specific grm identified by grm name

content:

  • key strings
word example type variable type variable values default explanation
file file: mygrm.csv compulsory word file name none content determines the name of the file containing the grm. mutually exclusive with keyword genotype.
genotype genotype: mygn compulsory word genotype name none content determines the genotype element to be used for building the grm. mutually exclusive with keyword file.
cross cross: mycross.csv optional word file name none content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.
pedigree pedigree: myped optional word pedigree name none content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.
method method:YA optional alternative words VR|YA VR content determines the method to be used for building a grm from genotypes
  • VR: VanRaden Method 1 is used
  • YA: VanRaden Method 2(method Yang) is used

<vars>

Example host type purpose 
<root>
 ..
 <vars>
  vars: g,p
  ...
 </vars>
</root>
 root compulsory hosts one to several elements each containing information about a specific variance.

content:

  • key strings
word example type variable type variable values default explanation
vars vars: g,p compulsory csv word-list variance names none list content determines names of nominated-compulsory elements
  • nominated-compulsory elements
  • compulsory element <res>

<res>

Example host type purpose 
<root>
 ..
 <vars>
  ..
  <res>
   <sigma>
    ..
   </sigma>
  </res>
  ..
 </vars>
</root>
 vars compulsory hosts information about the residual variance structure.

content:

  • compulsory element <sigma>
  • optional element <gamma>

<variance name>

Example host type purpose 
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <sigma>
    ..
   </sigma>
   <gamma>
    ..
   </gamma>
  </myvar>
  ..
 </vars>
</root>
 vars nominated-compulsory hosts information about variance structure identified by variance name.

content:

  • compulsory element <sigma>
  • optional element <gamma>

<sigma>

Example host type purpose 
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <sigma>
    ..
   </sigma>
   ..
  </myvar>
  ..
 </vars>
</root>
 variance name compulsory hosts information about $$\Sigma$$ as part of $$\Gamma \otimes \Sigma$$.

content:

  • key strings
word example type variable type variable values default explanation
file file: mymatrix.csv compulsory word file name none content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with <matrix attributes="array">.
type type: block optional word block none determines that $$\Sigma$$ is equal to $$\Theta$$
  • optional element <matrix attributes="array">

<gamma>

Example host type purpose 
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <gamma>
    ..
   </gamma>
   ..
  </myvar>
  ..
 </vars>
</root>
 variance name optional hosts information about $$\Gamma$$ as part of $$\Gamma \otimes \Sigma$$.

content:

  • mutually exclusive elements <A>, <H> and <E>

<A>

Example host type purpose 
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <gamma>
    <A>
     pedigree: myped
    </A>
   </gamma>
   ..
  </myvar>
  ..
 </vars>
</root>
 gamma compulsory hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree pedigree name.

content:

  • key strings
word example type variable type variable values default explanation
pedigree pedigree: myped optional word pedigree name none content determines the name of a pedigree previously invoked to be used to construct A.

<H>

Example host type purpose 
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <gamma>
    <H>
     type: tblup
     pedigree: myped
     genotype: mygn
     aweight: 0.05
     switch: adjustg2a
    </H>
   </gamma>
   ..
  </myvar>
  ..
 </vars>
</root>
 gamma compulsory hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree pedigree name and genomic information. the genomic information can be supplied
  • via a grm element for single step H-BLUP models
  • via a genotype element for single step T-BLUP models

content:

  • key strings
word example type variable type variable values default explanation
pedigree pedigree: myped compulsory word pedigree name none content determines the name of a pedigree element to be used to construct H.
type type: tblup optional word tblup|hblup hblup content determines the way the inverse of H is constructed.
grm grm: mygrm compulsory word pedigree name none content determines the grm element to be used to construct H. compulsory for hblup.

<E>

<model>

<eqn>

<poly>

<jobs>

Example: 

<root>
 ..
 <jobs>
  jobs: solve,yh
  ...
 </jobs>
</root>

host: root

content:

  • key strings
example type variable type variable values default explanation
jobs: solve,yh compulsory csv word-list solve,sample,pevsample,mcemreml,yh none job sequence is determined by the list sequence. list content determines nominated-compulsory elements
  • nominated-compulsory elements

<solve>

Example: 

<root>
 ..
 <jobs>
  ..
  <solve>
   solver: mysolver
  </solve>
  ..
 </jobs>
 ..
</root>

host: jobs

content:

  • key strings
example type variable type variable values default explanation
solver: mysolver compulsory word solver name none solver name must be the name of a previously defined solver

<sample>

<pevsample>

<mcemreml>

<yh>

<samplers>

<sampler name>

<solvers>

  • host: root

<solver name>

  • host: solvers
  • hosts mutually exclusive elements of which hard-coded names define the solver type

<pcgiod>

  • host: solver name
  • defines the solver is an iteration-on-data preconditioned gradient solver
element name element type host element hosts elements element function key string key word key string variable key string function key string type
pedigrees Automatic-optional root yes host elements of specific pedigrees pedigrees pedigree names nominates further elements compulsory
pedigree name Nominated-compulsory pedigrees no host information about a specific pedigree file pedigree file name provides pedigree file name compulsory
switch probabilistic pedigree is probabilistic optional
selfing pedigree contains selfing
phantomparents integer provides the number of individuals at the top of the pedigree which are phantom parents optional
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