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Last Login: Monday, January 15, 2007
Posts: 1,
Visits: 3
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I have recently found this great program and have a few questions. We work with canine genetics and our goal is to map new disease genes for various inherited diseases in dogs. One method we use, is linkage analysis and therefore we need linkage files from our pedigrees like this: 1 1 0 0 1 1 0 0 0
1 2 0 0 2 2 0 0 2
1 3 0 0 2 1 0 0 2
1 4 0 0 1 2 0 0 2
1 5 0 0 2 1 0 0 2
1 6 1 2 1 1 0 0 2
1 7 1 2 2 2 0 0 2
1 8 0 0 1 1 0 0 2
1 9 0 0 2 1 0 0 2
1 10 4 3 2 1 0 0 2
1 11 4 3 1 2 0 0 2
1 12 4 3 1 2 0 0 2
1 13 4 5 1 1 0 0 2
1 14 0 0 1 1 0 0 0
1 15 8 7 2 2 0 0 2
1 16 8 7 2 2 0 0 2
1 17 8 7 2 2 0 0 2
1 18 8 7 2 2 0 0 2
1 19 8 7 2 1 0 0 2
1 20 8 9 1 1 0 0 2
1 21 8 9 2 2 0 0 2
1 22 8 10 2 2 0 0 2
1 23 8 10 1 2 0 0 2
1 24 8 10 1 1 0 0 2
1 25 14 29 1 2 0 0 2
1 26 14 29 2 1 0 0 2
1 27 14 29 2 2 0 0 2
1 28 14 29 2 2 0 0 2 First number is the family number, second individual number, third is the id of father, 4th the id of mother, 5th gender (1= male, 2=female), 6th disease (0=unknown, 1=healthy, 2=ill), 7th and 8th loci 1 alleles and 9th DNA (0=not available, 2=available for genotyping). This is an example of data needed for simulation the data with SLINK. Would it be possible to generate directly this kind of file from the pedigree and vice versa? The availability of DNA would be nice to see somehow on pedigree picture. After genotyping, the alleles would be nice to see in pedigree, maybe under the gender symbol... My collague wishes a data field for dog registration number and was also wondering, if it is possible to adjust the affected symbol so, that instead of the "plus-sign" the symbol would be black? Hope you understand my english... Best regards, Paivi
Edited: Monday, January 15, 2007 by
GenoProSupport
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Gamma
FamilyTrees.GenoPro.com
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GenoPro version: 3.1.0.1
Last Login: 2 days ago @ 11:01 PM
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First, let me display for your data in a tabular format: | idFamily | idDog | idFather | idMother | Gender | Disease | Loci1 | Loci2 | DNA | | 1 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | | 1 | 2 | 0 | 0 | 2 | 2 | 0 | 0 | 2 | | 1 | 3 | 0 | 0 | 2 | 1 | 0 | 0 | 2 | | 1 | 4 | 0 | 0 | 1 | 2 | 0 | 0 | 2 | | 1 | 5 | 0 | 0 | 2 | 1 | 0 | 0 | 2 | | 1 | 6 | 1 | 2 | 1 | 1 | 0 | 0 | 2 | | 1 | 7 | 1 | 2 | 2 | 2 | 0 | 0 | 2 | | 1 | 8 | 0 | 0 | 1 | 1 | 0 | 0 | 2 | | 1 | 9 | 0 | 0 | 2 | 1 | 0 | 0 | 2 | | 1 | 10 | 4 | 3 | 2 | 1 | 0 | 0 | 2 | | 1 | 11 | 4 | 3 | 1 | 2 | 0 | 0 | 2 | | 1 | 12 | 4 | 3 | 1 | 2 | 0 | 0 | 2 | | 1 | 13 | 4 | 5 | 1 | 1 | 0 | 0 | 2 | | 1 | 14 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | | 1 | 15 | 8 | 7 | 2 | 2 | 0 | 0 | 2 | | 1 | 16 | 8 | 7 | 2 | 2 | 0 | 0 | 2 | | 1 | 17 | 8 | 7 | 2 | 2 | 0 | 0 | 2 | | 1 | 18 | 8 | 7 | 2 | 2 | 0 | 0 | 2 | | 1 | 19 | 8 | 7 | 2 | 1 | 0 | 0 | 2 | | 1 | 20 | 8 | 9 | 1 | 1 | 0 | 0 | 2 | | 1 | 21 | 8 | 9 | 2 | 2 | 0 | 0 | 2 | | 1 | 22 | 8 | 10 | 2 | 2 | 0 | 0 | 2 | | 1 | 23 | 8 | 10 | 1 | 2 | 0 | 0 | 2 | | 1 | 24 | 8 | 10 | 1 | 1 | 0 | 0 | 2 | | 1 | 25 | 14 | 29 | 1 | 2 | 0 | 0 | 2 | | 1 | 26 | 14 | 29 | 2 | 1 | 0 | 0 | 2 | | 1 | 27 | 14 | 29 | 2 | 2 | 0 | 0 | 2 | | 1 | 28 | 14 | 29 | 2 | 2 | 0 | 0 | 2 |
In GenoPro, you can feed XML content and have GenoPro draw your pedigree for you. The table above can be converted to XML easily. 1. Each individual can be stored in an XML element.
2. You replace the Gender values: 1=M, 2=F.
3. To draw the disease, you may pick a color you wish: 1=green (healthy), 2=red (ill).
4. Store the DNA value as-is. GenoPro will import the value as a custom tag.
5. Now the fun part is to link all of those individuals together. This is where the PedigreeLink element comes together. For this, you need to create a family object (this is not the same as your idFamily, but an architectural design of GenoPro). Next, you create a pedigree link to the family <Individual ID="1">
<Gender>M</Gender>
<Display.Colors.Gender.Fill="#00FF00" />
<DNA>0</DNA>
</Individual>
<Individual ID="2">
<Gender>F</Gender>
<Display.Colors.Gender.Fill="#FF0000" />
<DNA>2</DNA>
</Individual>
<Family ID="fam001" />
<PedigreeLink PedigreeLink="Parent" Family="fam0001" Individual="1" />
<PedigreeLink PedigreeLink="Biological" Family="fam0001" Individual="2" /> |
After importing, you should view a graphical pedigree in GenoPro with the colors for each disease. To add the dog registration number, you need to use custom tags (Menu -> Tools -> Tag Editor). From the Tag Editor, you should type the following layout: 
When you double-click on a individual (dog), you will see the following custom tag where you can enter your data: 
GenoPro display a custom tag on the pedigree and in the Table Layout. 
What is most interesting is you can generate a report and include the DNA and dog registration number in it. GenoPro's report generator can also connect to an external SQL database, so you can fetch additional DNA information for your report.
Edited: Thursday, January 18, 2007 by
GenoProSupport
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Gamma
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FamilyTrees.GenoPro.com
Translator
GenoPro version: 3.1.0.1
Last Login: Thursday, February 29, 2024
Posts: 257,
Visits: 2,858
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This explanation or form of it might be included in help, as database implementation in Genopro...
- "εν οιδα οτι ουδεν οιδα" (Σωκρατησ) - "The only thing that I know is that I don't know anything" (Socrates)
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Customers
GenoPro version: 2.0.0.2
Last Login: Thursday, February 22, 2007
Posts: 1,
Visits: 3
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It would be very useful to get an XSD-file that explains more in detail what genopro requires to open an XML file. Which tags should be there, etc, in order write a little Perl script that can convert an export from a database to XML that genopro recognises (because there is no possibility to open just any XML file exported from a database). I'm also a researcher in biology, and I'm thrilled by the possibilities this program gives to visualise pedigrees, but right now I'm a little taken back by the somewhat meagre documentation and capabilities for importing data from other applications. I wouldn't want to do all the data entry again - when it's already there in another database (around 1000 bird individuals).
Cheers,
Toby
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