2.5 Pedigree file description statements

Any of the following statements can be placed either in the parameter file or in the top section of the pedigree file, above the file separator, `****'. Most parameters have default values, in which case the statement is usually not required.

allow pedigree size N

This statement overrides the program-defined maximum pedigree size (presently 20,000 individuals).

input pedigree size N

Here, N is the number of records to be read. It may be less than the actual number of individuals in the pedigree file.

input pedigree record names 3 [integers I] [reals J]

This specifies the numbers of entries in each line of the pedigree file. There must be three names (up to 12 alphanumeric characters each) identifying an individual and his or her parents. Optional integers include gender and phenotypic or discrete trait data. Real numbers could be covariates or quantitative trait values.

input pedigree record (father mother | mother father)

This statement specifies the order of parental names. `father mother' is the default.

input pedigree record gender (present | absent)

Gender, which follows the required triplet of names, is optional. If this statement is not included, the default is `gender present'. Gender is coded as an integer, such that `1', `2' and `0' represent male, female, and unsexed, respectively.

input pedigree record observed (absent | present)

The observed indicator designates which members of the pedigree are observed and which are unobserved, indicated by `1' and `0', respectively. When the observed indicator is present, it follows gender (or parents if gender is not present). If this statement is absent, all pedigree members are assumed to be observed.

input pedigree record traits K1 K2... integers I1 I2...

This statement is needed when integer data for traits are included, and the trait values do not immediately and consecutively follow gender (if present). Use this statement to specify the correspondence between trait numbers and integers in the record.

Below are the first several lines of the sample pedigree file, `ped73.ped' in `MORGAN_Examples'.

input pedigree size 73 input pedigree record names 3 integers 6 reals 1 *************************************************** 101 0 0 1 0 0 0 -1 -1 999.5 102 0 0 2 0 0 0 -1 -1 999.5 201 101 102 1 0 0 0 0 1 999.5

Note that genotype data are not contained in the pedigree file; genotype data, if required for the MORGAN program invoked, are contained in the parameter file or in a marker data file specified in the parameter file using the `input marker data file' statement. The second parameter statement in the file, `input pedigree record names 3 integers 9 reals 1' describes the format of the data on each line (also called a record) in the file. The first three values in each row, the names, give an individual's identification number followed by those of his or her father, then mother. Because there is no `input pedigree record gender' statement, gender is assumed to be present and to directly follow the three names. Absence of an `input pedigree record observed' statement means that all individuals are assumed to be observed. The 8 integers following gender and the real number in the final column represent trait data. Lack of an `input pedigree record traits integers' statement indicates that the first integer following gender corresponds to trait 1, the second to trait 2, etc. These (and other) parameter statement defaults apply only if there is no overriding statement in any of the parameter files used. Programs will generally provide a warning statement (coded "(W)") when default values are being used due to absence of a relevant parameter statement.