- Overview
At any time, DNA·VIEW can be asked to compile an
allele frequency database, based on accumulated profiles.
Take a look at VII.A.3 so that you have an idea of how the program will view your data.
The genotypes of anyone with an accession number can be included in the database.
That certainly includes anyone in a Case (Paternity, Kinship, etc.),
but more generally anyone who occurs on a (membrane) roster even if they are not used
in any Case.
Any single database pertains to
- one specified locus
- one or more specified race letters.
That is, people are chosen for inclusion
according to the race letter that is part of the
definition of that person. In fact, selection for
inclusion in a database is the whole reason for
associating a race letter with a person. (The
specification of the race to be used for calculation
comes from a race letter associated with a Case,
or sometimes chosen by the user in response to a prompt.)
- a range of accession (person) numbers.
most often I select the full range of accession numbers from
80-00000
to 9999-99999
, but if perchance you
have in mind to create many categories for population studies,
advance planning of your accession number scheme may be helpful.
- a set of "Reader numbers"
The default, usually most useful is to use all of them (099=Genotyper might be the only
one), except for 000=Student.
- Preparation
- Routine
So keep the above in mind while designing data encoding and
calculating cases. In particular, you probably want to reserve
particular letters for the likely races of interest e.g.
p for Puerto Rican. Then, every man
and every woman (but preferably not the children) should have the
letter attached to their person-description.
There are a few ways of doing this. You may want to use a combination.
- Assign race to an entire worklist
With Assign race to membrane ( menu)
- select a collection of membranes/worklists;
- say whether to exclude children (probably yes);
- choose some race (letter) such as p.
Then all the denominated people will be assigned to the desired race.
- Assign race to people in a case
For each case, select the case (in Paternity case), choose edit people,
and the editing cursor will appear on the first person, the mother.
- space twice to go past the accession number
- type e.g. p in the race cell
- tab to skip to the next person
- tab to skip past a child
- fix the (alleged) father(s) in the same way as the mother.
The most efficient practice is to make a habit of doing this while
you are computing the cases. Then the data is ready to create
databases whenever you like.
- Assign race to individual people in a worklist
- Open the worklist with Membrane from the menu.
- Select the lane with the person of interest.
- Space throught the fields to edit the person an introduce the desired race.
- Preliminary check
The Case List option (in Paternity Case)
can be used to quickly review a sequence of cases to check if you have
properly filled in the race letter for each person.
- Compile database
In fact, I wouldn't bother to wait for 100 cases, because once you
make them the first time to REbuild is extremely quick easy just
one operation for all 13 loci. See VII.A.5.c.
Initial creation of databases
Even with no cases at all, you can build the (empty) databases for your lab.
When you do it the first time, there is a separate operation for each locus,
so you will need 2 or 3 minutes to do all 13 (or so) loci.
The procedure is straightforward:
Step-by-step
- Populations
- Database
- Compile a new database from DNA·VIEW data
Which locus?
. Select the desired locus.
Which readers?
. Enter for default choice(s).
Which race(s)?
. Type 1 to 6 letters designating races to
be include in the database, Enter
Earliest acceptable accession ID 80-0000
.
Enter to accept the default
Last acceptable accession ID 9999-0000
.
Enter to accept the default
- (time passes, probably a few seconds, and counters indicate progress as the program
finds and compiles the relevant data)
Select the database to update, or End to make a new one
and the list of already existing databases is displayed. Usually,
End to add a new database to the list.
- Esc to proceed to the next locus.
Updating the databases
Once the databases have been built the first time, they can easily later be
updated to reflect additional people who have been entered into DNA·VIEW.
There are two easy ways to do this. The first method assumes that you have
marked as defaults the databases that you want to update. If you've
already been using them for casework, then this would be the case. Or, if you're
planning to use them for casework after the re-compilation, then go ahead and
mark them as defaults now, the proceed with re-compilation.
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Step-by-step (re-compile default databases)
- Populations
- Database
- Update the default databases (but only those marked
as from your own laboratory)
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The second method is more general, but takes (just) a few more keystrokes:
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Step-by-step (recompile arbitrary list of databases)
- Populations
- Database
- Update arbitrary list of databases
Select databases to update
Accept lines containing My lab
Enter to limit the list to "My lab"'s databases.
Select databases to update
Accept lines containing
If desired to restrict the list further, type a context then Enter
Select databases to update
Accept lines containing
Enter to proceed with the compilation.
- Obtain and drink coffee
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