The PBAT pedigree and
phenotype files:
- Following
the FBAT convention, PBAT pedigree files
have the extension “.ped”.
- The
first line of the PBAT pedigree file
contains the names of the markers.
- From
the second line on, the pedigree file contains the pedigree data. Each
line stands for one individual/subject. Each line of the pedigree file
starts with the pedigree id, followed by the individual/subject id, the id
of the father, the id of the mother, the individual’s sex and affection
status. After this information, for each marker, both marker alleles are
listed. The order of the markers has to correspond to the order of the
marker names in the first line of the file.
The coding
of missing values in the pedigree and the phenotype file for PBAT
- In the
pedigree file, missing alleles, unknown affection status and unknown sex
are coded as “0”.
- If an
individual’s mother or father is referred to in the pedigree file, but
does not have its own entity in the pedigree file, PBAT assumes
that her/his marker alleles are missing.
- Missing
values in the phenotype file have to be coded either as “.” or “-”. Coding missing phenotypes as “0” will
lead to incorrect results.
Examples for
PBAT pedigree and
phenotype:
The pedigree file “example.ped” and phenotype file “example.phe”
have been simulated. The “example.ped”-file contains
one marker with the alleles “1” and “2”. All families in this example are
trios. The “example.phe”-file
contains four phenotypes, i.e. “pheno1”, “pheno2”, “pheno3” and “pheno4”, two
covariate/predictor variables, i.e. “covariate1” and “covariate2”, and one
exposure variable “exposure” that is coded as “0” and “1”.
PGA examples: