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3.1 Introduction to pedcheck
3.2 Sample pedcheck
parameter file3.3 Running pedcheck
examples3.4 pedcheck
statements
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pedcheck
pedcheck
reads the pedigree file and checks for errors in the pedigree
structure. Specifically, it checks for the following errors:
Note that, unlike some other packages, name identifiers must be unique across the entire data set, not only within pedigree components. If using pedigree files from other packages we recommend that new name identifiers be created if necessary, for example by combining pedigree (family) and individual identifiers: for example `pedname_indname'. In MORGAN names are arbitrary strings (subject to no whitespace) up to 15 characters in length to accommodate this translation easily.
If no errors are found, pedcheck
reports the number of components
(connected pedigrees) found and lists for each component:
If there are changes to the file, pedcheck
writes an output pedigree
file. Requested changes may include reordering of the pedigree chronologically
(by component, then by individual), the addition of gender, the addition of an
observed indicator, and reversing the order of the parental names.
Other MORGAN programs do their own pedigree checking by calling the
relevant pedcheck
functions, but it is still useful to do preliminary
processing of data files first.
See Concept Index for:
pedcheck
introduction,
pedigree validity,
component.
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pedcheck
parameter file
Files for pedcheck
may be found in the `Pedcheck' subdirectory of
`MORGAN_V30_Examples'. Below is the sample parameter file `check.par' for
pedcheck
:
set printlevel 5 input pedigree file `check.ped' input pedigree size 30 input pedigree record gender absent input pedigree record observed present assign gender output pedigree chronological output overwrite pedigree file `check.oped' |
The `assign gender' statement requests that pedcheck
determine
gender, when possible, and output that information to the output pedigree file.
The gender determination is made based on the default order for the listing of
parents, which is father followed by mother. Individuals who are not parents
will be assigned missing gender, `0'.
`output pedigree chronological'
causes the pedigree to be sorted into chronological order in the output pedigree
file, first by component, then by individual name. MORGAN refers to
each connected pedigree (i.e., distinct family) in a file as a component.
The first individual in the input listing who is not genealogically connected to
individual 1 defines component 2, and the first who is not connected to either
of these defines component 3, etc. Although pedcheck
groups individuals
by their MORGAN--assigned component numbers in the output pedigree
file, it does not list the component numbers. That is, the first three columns
of the output file are just as they were in the input file: individual name,
father's name, mother's name.
`output overwrite pedigree file `check.oped'' specifies the output pedigree file. The overwrite option permits a previously existing `check.oped' to be overwritten. You should be cautious is using this option, in order not to overwrite files you wish to keep. However, if this option is not used, you will get an error message and the program will quit if `check.oped' already exists. If this occurs, you may delete the file and try again or use another output file name.
See Concept Index for:
pedcheck
sample parameter file,
component,
pedigree component,
overwrite file options.
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pedcheck
examples
Examples for the program pedcheck
are under the subdirectory
`Pedcheck/'. The commands using example files are listed below. Have a
look inside the pedigree and parameter files, then verify that the output files
are as you would expect them to be. If error messages are generated, verify
that they make sense and see if you can make the necessary corrections so that
pedcheck
will run.
runs on input pedigree file `check.ped'. The pedigree contains no errors, but has no gender specified and is not in chronological order. Look at the parameter file: you will see that it specifies the absence of gender, and requests that gender be assigned and that the output pedigree be chronologically ordered. Then, indeed, the output pedigree file `check.oped' has gender assigned and has the members reordered. Notice that individuals who are not parents (531 and 541) have missing gender, `0', in the fourth column of `check.oped'. The overwrite option permits a previously existing `check.oped' to be overwritten.
runs on input pedigree file `imp.ped'. The pedigree contains an individual who is his own ancestor.
runs with an empty parameter file, apart from a `set printlevel 5' request. The input pedigree file `sex.ped' is specified on the command line. What does the output say is wrong with this pedigree?
runs with an empty parameter file, with input pedigree file `dup.ped' specified on the command line. What does the output say is wrong with this pedigree?
See Concept Index for:
pedcheck
examples.
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pedcheck
statements
pedcheck
statements apply to other MORGAN programs since the
programs call the pedcheck
functions first to check the pedigree file
before doing computations on the pedigree data.
(assign | ignore) gender
Optional. `assign gender' causes gender to be determined by parentage, whether or not gender is included in the pedigree file. `ignore gender', causes the program to not check or assign gender. The default action is to assign gender when it is absent and to check gender if it is present.
output pedigree chronological
Optional. If this statement is present and if the input file is not in chronological order, the pedigree is sorted and written out in chronological order. The pedigree is sorted by components, and within each component, each non-founding member is preceded by her or his parents. If this statement is not given, the input order is preserved in the output file, if written. See the previous section of this chapter for further discussion of pedigree components.
output pedigree record (father mother | mother father)
Optional. This statement causes the parents to be named in the specified order. The default arrangement for each triplet of names is the input order.
See Concept Index for:
pedcheck
statements,
pedcheck
statements,
pedigree options,
gender,
pedigree order,
component,
pedigree component.
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