PEDFILE(5)

NAME
PEDFILE - LINKAGE's PEDFILE, Pedigree Information

DESCRIPTION
In addition to phenotypes and description of loci, the LINKAGE programs require pedigree information in order to traverse the pedigree when calculating the likelihood. The input must contain the following information for each individual:

•   a pedigree number

•   an individual identification number, or id

•   father's id number

•   mother's id number

•   first offspring id number

•   next paternal sibling id number

•   next maternal sibling id number

•   sex

•   "proband status"

The first offspring can be any of an individual's children, but the next sib id's for the offspring will be constrained by this choice. The next-paternal-sibling and next-maternal-sibling numbers, along with first-offspring number, provide a set of pointers to pass from one child to the next. The first offspring of the father is any of his children; the next paternal sib of the first offspring is any other of his children, etc. The entry for the next paternal sib of the last child is "0". Similar pointers are made for the mother's children. For full-sibs, it is convenient to make id's for the next maternal and next paternal siblings identical, but when one or both parents have children from different marriages, at least some will have different values. Father and mother id's are 0 for founders, or other members of the pedigree for whom information on parents is absent. Otherwise, both parents must be present in the pedigree even if one is unknown. If one parent is unknown, an id number must still be created, and a record for the fictitious parent must appear in the pedigree file. The "proband" refers to a starting individual for linkage calculations (indicated by a 1 in the proband field). The choice of the proband is not necessarily related to the ascertainment of the pedigree; indeed, it is usually more efficient to calculate from a founding ancestor rather than from the true proband. Risks are also calculated for the person designated as the proband. Other individuals should have a 0 in the proband field, except in pedigrees containing inbreeding or marriage loops as discussed in section 2.8. If no proband is designated, the first individual encountered for a pedigree will be used as a starting point for the calculation. The sex field is coded 1 for males and 2 for females. These default values can be changed by modifying a program constant. The creation of the first offspring, next maternal sib and next paternal sib pointers is done automatically by the program MAKEPED (not covered in this document). The input to the MAKEPED program is a file with individual records containing the pedigree number, id number, father id, mother id, sex and phenotypic data. The phenotypic data are coded as discussed in LINKAGE(5) and in the following examples. The MAKEPED program also allows automatic selection of probands for efficient likelihood calculations.

EXAMPLE
Consider the pedigree shown in Figure 1. Data on three loci are presented: one disease locus and two marker loci. An "a" below an individual stands for "affected," and "u" stands for unknown. The first marker locus has three alleles present in the pedigree, while the second has two alleles present.
                       [1]--.--(2)
                        a |
                        22 | 12
                        12 | 12
         Figure 1 |
                     .------+------.
                     | | |
            (6)--.--[3] [4] (5)
                 | a
             13 | 12
             12 | 22
                 |
             .-------.
             | |
            [7] (8)--.--(10)
             a |
             13 u | 12
             22 u | 12
                        |
                        (9)
                        a
                        11
                        12 The input PEDFILE can take the following form:
1 | 1 | 0 | 0 | 3 | 0 | 0 | 1 | 1 | 2 | 0 | 1 | 0 | 1 | 1 | Ped: 1 Per: 1
1 | 2 | 0 | 0 | 3 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | Ped: 1 Per: 2
1 | 3 | 1 | 2 | 7 | 4 | 4 | 1 | 0 | 2 | 1 | 1 | 0 | 0 | 1 | Ped: 1 Per: 3
1 | 4 | 1 | 2 | 0 | 5 | 5 | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | Ped: 1 Per: 4
1 | 5 | 1 | 2 | 0 | 0 | 0 | 2 | 0 | 2 | 1 | 1 | 0 | 0 | 1 | Ped: 1 Per: 5
1 | 6 | 0 | 0 | 7 | 0 | 0 | 2 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | Ped: 1 Per: 6
1 | 7 | 3 | 6 | 0 | 8 | 8 | 1 | 0 | 2 | 1 | 0 | 1 | 0 | 1 | Ped: 1 Per: 7
1 | 8 | 3 | 6 | 9 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | Ped: 1 Per: 8
1 | 9 | 8 | 10 | 0 | 0 | 0 | 2 | 0 | 2 | 1 | 0 | 0 | 1 | 1 | Ped: 1 Per: 9
1 | 10 | 0 | 0 | 9 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | Ped: 1 Per: 10
The PEDFILE has been produced from an input file by the MAKEPED program. The comments at the end of each record indicate original pedigree and id codes. The first entry in each record is followed by the pedigree number, id number, five pedigree pointers (father id, mother id, first offspring id, next paternal sib id, next maternal sib id), sex, proband, disease status, and marker loci coded as binary factors. Comparison with the original pedigree will reveal the coding scheme. Individual 1 has been chosen as the "proband;" as this is the first individual of this pedigree encountered in the file, the entry in the proband field is optional. Now consider the same pedigree extended to include some half sibs (Figure 2).
                        [1]--.--(2)
                        a |
          Figure 2 22 | 12
                        12 | 12
                        |
                        .------+------.
                        | | |
                       (6)--.--[3] [4] (5)
                        | a a
                        13 | 12 22 12
                        12 | 22 12 22
                        |
               .-------------------------.
               | |
     (11)--.--[7]--.--(12)--.--[13] (8)--.--(10)
           | a | | |
      u | 13 | 12 | u u | 12
      u | 22 | 12 | u u | 12
           | | | |
          (14) (15) (16) (9)
                        a
           13 13 11 11
           12 12 12 12 The MAKEPED program produces the following file for this pedigree (figure 2):
1 | 1 | 0 | 0 | 3 | 0 | 0 | 1 | 1 | 2 | 0 | 1 | 0 | 1 | 1 | Ped: 1 | Per: 1
1 | 2 | 0 | 0 | 3 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | Ped: 1 | Per: 2
1 | 3 | 1 | 2 | 7 | 4 | 4 | 1 | 0 | 2 | 1 | 1 | 0 | 0 | 1 | Ped: 1 | Per: 3
1 | 4 | 1 | 2 | 0 | 5 | 5 | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | Ped: 1 | Per: 4
1 | 5 | 1 | 2 | 0 | 0 | 0 | 2 | 0 | 2 | 1 | 1 | 0 | 0 | 1 | Ped: 1 | Per: 5
1 | 6 | 0 | 0 | 7 | 0 | 0 | 2 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | Ped: 1 | Per: 6
1 | 7 | 3 | 6 | 14 | 8 | 8 | 1 | 0 | 2 | 1 | 0 | 1 | 0 | 1 | Ped: 1 | Per: 7
1 | 8 | 3 | 6 | 9 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | Ped: 1 | Per: 8
1 | 9 | 8 | 10 | 0 | 0 | 0 | 2 | 0 | 2 | 1 | 0 | 0 | 1 | 1 | Ped: 1 | Per: 9
1 | 10 | 0 | 0 | 9 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | Ped: 1 | Per: 10
1 | 11 | 0 | 0 | 14 | 0 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | Ped: 1 | Per: 11
1 | 12 | 0 | 0 | 15 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | Ped: 1 | Per: 12
1 | 13 | 0 | 0 | 16 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | Ped: 1 | Per: 13
1 | 14 | 7 | 11 | 0 | 15 | 0 | 2 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | Ped: 1 | Per: 14
1 | 15 | 7 | 12 | 0 | 0 | 16 | 2 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | Ped: 1 | Per: 15
1 | 16 | 13 | 12 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 0 | 0 | 1 | 1 | Ped: 1 | Per: 16

The following data refer to a larger pedigree, taken from a coronary heart disease study, in PEDFILE form:
1 | 1 | 0 | 0 | 3 | 0 | 0 | 2 | 0 | 2 | 3 | 0 | 0 | 0.00 | Ped: 1 | Per: 1
1 | 2 | 0 | 0 | 3 | 0 | 0 | 1 | 1 | 2 | 3 | 0 | 0 | 0.00 | Ped: 1 | Per: 2
1 | 3 | 2 | 1 | 7 | 5 | 5 | 1 | 0 | 2 | 2 | 0 | 0 | 0.00 | Ped: 1 | Per: 3
1 | 4 | 0 | 0 | 7 | 0 | 0 | 2 | 0 | 1 | 2 | 0 | 0 | 0.00 | Ped: 1 | Per: 4
1 | 5 | 2 | 1 | 21 | 0 | 0 | 2 | 0 | 1 | 3 | 0 | 1 | 22.70 | Ped: 1 | Per: 5
1 | 6 | 0 | 0 | 21 | 0 | 0 | 1 | 0 | 2 | 3 | 0 | 0 | 0.00 | Ped: 1 | Per: 6
1 | 7 | 3 | 4 | 26 | 9 | 9 | 1 | 0 | 2 | 2 | 0 | 0 | 0.00 | Ped: 1 | Per: 7
1 | 8 | 0 | 0 | 26 | 0 | 0 | 2 | 0 | 1 | 2 | 0 | 1 | 9.20 | Ped: 1 | Per: 8
1 | 9 | 3 | 4 | 31 | 11 | 11 | 1 | 0 | 2 | 2 | 1 | 1 | 24.30 | Ped: 1 | Per: 9
1 | 10 | 0 | 0 | 31 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 0 | 9.30 | Ped: 1 | Per: 10
1 | 11 | 3 | 4 | 0 | 12 | 12 | 1 | 0 | 2 | 2 | 1 | 1 | 23.90 | Ped: 1 | Per: 11
1 | 12 | 3 | 4 | 34 | 14 | 14 | 1 | 0 | 2 | 2 | 1 | 1 | 20.70 | Ped: 1 | Per: 12
1 | 13 | 0 | 0 | 34 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 0 | 14.50 | Ped: 1 | Per: 13
1 | 14 | 3 | 4 | 0 | 15 | 15 | 2 | 0 | 1 | 2 | 1 | 0 | 2.10 | Ped: 1 | Per: 14
1 | 15 | 3 | 4 | 40 | 17 | 17 | 1 | 0 | 2 | 2 | 0 | 0 | 0.00 | Ped: 1 | Per: 15
1 | 16 | 0 | 0 | 40 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 1 | 9.80 | Ped: 1 | Per: 16
1 | 17 | 3 | 4 | 43 | 19 | 19 | 1 | 0 | 2 | 2 | 0 | 0 | 0.00 | Ped: 1 | Per: 17
1 | 18 | 0 | 0 | 43 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 0 | 11.50 | Ped: 1 | Per: 18
1 | 19 | 3 | 4 | 0 | 0 | 0 | 1 | 0 | 1 | 2 | 1 | 0 | 9.20 | Ped: 1 | Per: 19
1 | 20 | 0 | 0 | 47 | 0 | 0 | 2 | 0 | 0 | 1 | 0 | 0 | 0.00 | Ped: 1 | Per: 20
1 | 21 | 6 | 5 | 47 | 22 | 22 | 1 | 0 | 2 | 2 | 0 | 0 | 0.00 | Ped: 1 | Per: 21
1 | 22 | 6 | 5 | 48 | 24 | 24 | 1 | 0 | 2 | 2 | 0 | 0 | 0.00 | Ped: 1 | Per: 22
1 | 23 | 0 | 0 | 48 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 0 | 13.40 | Ped: 1 | Per: 23
1 | 24 | 6 | 5 | 0 | 25 | 25 | 2 | 0 | 1 | 2 | 1 | 1 | 10.40 | Ped: 1 | Per: 24
1 | 25 | 6 | 5 | 0 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 1 | 9.90 | Ped: 1 | Per: 25
1 | 26 | 7 | 8 | 0 | 27 | 27 | 2 | 0 | 1 | 2 | 1 | 1 | 16.80 | Ped: 1 | Per: 26
1 | 27 | 7 | 8 | 53 | 29 | 29 | 2 | 0 | 1 | 2 | 0 | 1 | 30.10 | Ped: 1 | Per: 27
1 | 28 | 0 | 0 | 53 | 0 | 0 | 1 | 0 | 1 | 2 | 1 | 0 | 6.90 | Ped: 1 | Per: 28
1 | 29 | 7 | 8 | 56 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 1 | 15.40 | Ped: 1 | Per: 29
1 | 30 | 0 | 0 | 56 | 0 | 0 | 1 | 0 | 1 | 2 | 1 | 0 | 14.30 | Ped: 1 | Per: 30
1 | 31 | 9 | 10 | 0 | 32 | 32 | 2 | 0 | 1 | 1 | 1 | 0 | 6.80 | Ped: 1 | Per: 31
1 | 32 | 9 | 10 | 0 | 33 | 33 | 1 | 0 | 1 | 1 | 1 | 0 | 5.60 | Ped: 1 | Per: 32
1 | 33 | 9 | 10 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 1 | 31.60 | Ped: 1 | Per: 33
1 | 34 | 12 | 13 | 0 | 35 | 35 | 1 | 0 | 1 | 1 | 1 | 0 | 19.40 | Ped: 1 | Per: 34
1 | 35 | 12 | 13 | 0 | 36 | 36 | 2 | 0 | 1 | 1 | 1 | 1 | 41.70 | Ped: 1 | Per: 35
1 | 36 | 12 | 13 | 0 | 37 | 37 | 1 | 0 | 1 | 1 | 1 | 0 | 20.50 | Ped: 1 | Per: 36
1 | 37 | 12 | 13 | 0 | 38 | 38 | 1 | 0 | 1 | 1 | 1 | 1 | 28.40 | Ped: 1 | Per: 37
1 | 38 | 12 | 13 | 0 | 39 | 39 | 2 | 0 | 1 | 1 | 1 | 0 | 11.50 | Ped: 1 | Per: 38
1 | 39 | 12 | 13 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 21.00 | Ped: 1 | Per: 39
1 | 40 | 15 | 16 | 0 | 41 | 41 | 2 | 0 | 1 | 1 | 1 | 0 | 10.50 | Ped: 1 | Per: 40
1 | 41 | 15 | 16 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 12.60 | Ped: 1 | Per: 41
1 | 42 | 0 | 0 | 52 | 0 | 0 | 1 | 0 | 1 | 1 | 1 | 0 | 11.20 | Ped: 1 | Per: 42
1 | 43 | 17 | 18 | 52 | 44 | 44 | 2 | 0 | 1 | 1 | 1 | 1 | 37.20 | Ped: 1 | Per: 43
1 | 44 | 17 | 18 | 0 | 45 | 45 | 2 | 0 | 1 | 1 | 1 | 0 | 10.10 | Ped: 1 | Per: 44
1 | 45 | 17 | 18 | 0 | 46 | 46 | 1 | 0 | 1 | 1 | 1 | 1 | 34.90 | Ped: 1 | Per: 45
1 | 46 | 17 | 18 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 1 | 1 | 25.30 | Ped: 1 | Per: 46
1 | 47 | 21 | 20 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 1 | 47.90 | Ped: 1 | Per: 47
1 | 48 | 22 | 23 | 0 | 50 | 50 | 2 | 0 | 1 | 1 | 1 | 0 | 14.00 | Ped: 1 | Per: 48
1 | 49 | 0 | 0 | 51 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0.00 | Ped: 1 | Per: 49
1 | 50 | 22 | 23 | 51 | 0 | 0 | 2 | 0 | 1 | 2 | 1 | 1 | 55.30 | Ped: 1 | Per: 50
1 | 51 | 49 | 50 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 13.60 | Ped: 1 | Per: 51
1 | 52 | 42 | 43 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 12.50 | Ped: 1 | Per: 52
1 | 53 | 28 | 27 | 0 | 54 | 54 | 1 | 0 | 1 | 1 | 1 | 1 | 37.50 | Ped: 1 | Per: 53
1 | 54 | 28 | 27 | 0 | 55 | 55 | 1 | 0 | 1 | 1 | 1 | 1 | 14.70 | Ped: 1 | Per: 54
1 | 55 | 28 | 27 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 1 | 29.90 | Ped: 1 | Per: 55
1 | 56 | 30 | 29 | 0 | 57 | 57 | 1 | 0 | 1 | 1 | 1 | 0 | 5.70 | Ped: 1 | Per: 56
1 | 57 | 30 | 29 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 0 | 8.20 | Ped: 1 | Per: 57

Here, three loci are represented. The first is an affection status locus (coronary disease symptoms) with three liability classes (ages 0-20, 20-40, and greater than 40); the second is a binary factor locus (LDL receptor polymorphism), and the third is a quantitative variable (age adjusted LDL cholesterol levels). Individuals with unknown affection status are assigned to the first liability class in this example, but the results would be the same irrespective of this assignment.

NOTES
The information contained herein was gleaned, often-times verbatim, from the LINKAGE User's Guide (http://linkage.rockefeller.edu/soft/linkage/) on the web by kind permission of Jurg Ott, Ph.D.

AUTHORS
Mark Lathrop and Jurg Ott.

This manual page was written by Elizabeth Barham <lizzy@soggytrousers.net> for the Debian GNU/Linux distribution.

WORLD-WIDE-WEB
http://linkage.rockefeller.edu/soft/linkage/ (http://linkage.rockefeller.edu/soft/linkage/)

SEE ALSO
LINKAGE(5), DATAFILE(5), ilink(1), linkmap(1), lodscore(1), mlink(1), and unknown(1).