Phenotype file

Description

Phenotype file contains information about individual phenotype values: height, BMI, age, dichotomous trait, etc, and only for those which have phenotype data. If some person is missing phenotype data (e.g. unknown or phenotype value is not measured), PedConvert sets missing phenotype for those individuals.

Philosophy of using separate phenotype file

When phenotypes are stored in separate phenotype file and PedConvert is used to concatenate files:

1. Easy analysis of multiple phenotypes by just changing phenotype file with using --phen option.
2. If quantitative trait requires log, 1/x or other mathematical transformation, only one file needs to be modified, not all 23 pedigree files.

Format

Columns are: pedigree ID, person ID, Phenotype(s). Pedigree ID and Person ID must correspond to IDs in pedigree file. First line includes number of phenotypes and phenotype names. Columns are separated by space or tab characters.

    1     Age
    1  1  45
    1  3  56
    2  2  34
    2  3  67

Multiple phenotypes example (missing value is x):

    3     Height   Age   HDL
    1  1  167      34    2.3
    1  3  164      45    1.0
    2  2  198      78    x
    2  3  179      56    2.7

Dichotomous trait (unknown/missing value is 0):

    1     MARFAN
    1  1  1
    1  3  1
    2  2  2
    2  3  0

Dichotomous trait with liability class (unknown/missing value is 0):

    2     MARFAN     LIAB
    1  1  1          1
    1  3  1          1
    2  2  2          2
    2  3  0          2

If liability class is used, model file must include penetrances for all classes and --liab option must be specified!

In Merlin one can analyze multiple dichotomous traits at the same time. Two dichotomous traits (unknown/missing value is 0):

    2     MARFAN  MARFAN_SUB2
    1  1  1       0
    1  3  1       0
    2  2  2       2
    2  3  0       0

Last line of the file must be empty line!

Naming

Phenotype file is usually named as phen.dat.