Parameter file elements
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<pedigrees>
Example | host | type | purpose |
<root>
..
<pedigrees>
pedigrees: a,b
...
</pedigrees>
</root> |
root | automatic-optional | hosts one to several elements each containing information about a specific pedigree |
content:
- key strings
word | example | type | variable type | variable values | default | explanation |
pedigrees | pedigrees: a,b | compulsory | csv word-list | pedigree names | none | list content determines names of nominated-compulsory elements |
- nominated-compulsory elements
<pedigree name>
Example | host | type | purpose |
<root>
..
<pedigrees>
pedigrees: myped
..
<myped>
file: myped.csv
switch: selfing
phantomparents: 2
</myped>
..
</pedigrees>
</root> |
pedigrees | nominated-compulsory | hosts information about a specific pedigree identified by pedigree name |
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.
|
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
|
<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>
<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 |