Due to the manner in which a pedigree file is read by computer
programs one cannot include inline comments in the file as one can in the locus and BATCH2.DAT
files. Therefore this key file will explain the layout of the example file
PEDIGREE.DAT. For a more complete explanation of this format, please see the pedigree data format
file.
The first line in the PEDIGREE.DAT file is the format in which the pedigree header information is written.
In this example file: "(I5,1X,A8)". Here I5 indicates
an integer value occupying five spaces [which will be the number of people in the
pedigree to follow]; 1X indicates a blank space; and A8 indicates
a word occupying eight spaces [which will be the name of the pedigree to follow,
this name may be blank].
The second line is the format in which the data for each individual in a pedigree
is written. In this example: "(3A8,1X,2(A1,1X),A8,(T38,3(A8),:))".
Here 3A8 indicates three words occupying eight spaces each [the individual's
and the parents' names]; 1X indicates a blank space; 2(A1,1X) indicates
two one-character words [the individual's gender and the name of the set of monozygotic
twins to which this individual belongs] and each of these one-character words is
followed by a single space; A8 indicates a word occupying eight spaces [the
individual's trait phenotype]; (T38,...,:) indicates that the remainder
of the data will start at position 38 on the current and subsequent lines until the
data for this person is exhausted; and finally, 3(A8) indicates that the
remainder of the data are words, each occupying eight spaces, with at most three
words per line [all the individual's marker phenotypes and then any liability classification
and quantitative variables].
The third line is the header information for the first pedigree: the number of people
in the pedigree and then the pedigree's name, which may be blank. In this example:
9 PED#1
For each individual in the pedigree there follows a set of personal data. This data
includes in order: the individual's name; the names of the parents if they appear
in this pedigree, otherwise leave the parents' names blank; the individual's gender
(the gender code can be specified in the BATCH2.DAT file but by default
F=female and M=male); if the individual has any monozygotic twins in the pedigree,
then include here a name for this set of twins, otherwise leave this name blank;
the individual's trait phenotype, if applicable; in the same order as the markers
appear in the locus file, the marker phenotypes (all unknown phenotypes should consist
of blank spaces and of course genotype names may be substituted for any phenotypes);
and finally, any liability classification and quantitative variables (there are none
here). In this example:
1 F AFFECTED 5/4 5/7 3/4
7/8 2/3 3/4
1/2 3/5
2 M AFFECTED 4/5 5/5 2/9
4/6 1/2 1/1
4/5 4/5
3 2 1 F AFFECTED 4/4 5/5 4/9
7/6 3/1 4/1
1/5 5/5
4 2 1 F AFFECTED 4/5 5/5 4/9
7/6 3/1 4/1
1/4 5/4
5 2 1 F AFFECTED 4/4 7/5 3/2
8/4 2/2 3/1
2/5 3/5
6 2 1 F AFFECTED 5/5 5/5 4/2
7/4 3/2 4/1
2/4 3/4
7 2 1 F AFFECTED 4/4 7/5 3/9
8/6 3/1 4/1
1/4 5/4
8 M AFFECTED 5/5 5/5 9/9
8/4 2/2 7/5
5/1 4/4
9 8 7 F AFFECTED 4/5 7/5 3/9
8/4 3/2 4/7
1/1 5/4 After the last line of personal data for the previous pedigree, the next non-blank line is the header information for the next pedigree: number of people in the pedigree and the pedigree name. If there are no additional pedigrees, then end the file after the last line of personal data. Do not include any non-blank lines after the last line of data of the last pedigree.