PowQ
requires pedigree files and map files as input.
The
pedigree file describes the relationships between families’ members. Each row
of the file describes a single individual and has the following standard
format:
The
FamilyID is a numeric code that uniquely
identifies a family within a pedigree file.
The
PersonID is a numeric code that uniquely
identifies an individual within a family.
FatherID and MotherID are the numeric codes
that specify the individual’s parents. If an individual is a founder each
parent identifier field contains a “0”, otherwise the two parents should be
present in the same family.
All
fields must be separated by a single TAB.
.
An
example of a family where three sons are selected for the power study:
1 1 0 0 1 0
1 2 0 0 2 0
1 3 0 0 1 2
1 4 0 0 1 2
1 5 0 0 1 2
A
pedigree file can contain a single family or several families.
If
evaluating a study in order to estimate the power of a number of families
having the same structure, it is possible to specify a single family and ask
PowQ to simulate the data on a number of replicates of the same family
structure. When evaluating a comparative study, each individual in the pedigree
files must have a unique identifier within the whole file. The reason is
that if one wants, for instance, to investigate the effects on power derived
from the partitioning of a single large genealogy (or of very large different
families) in sub-pedigrees, the combined FamilyID
and PersonID fields could be not sufficient to
address the same individual in the two different pedigree files.
The
default extension for a pedigree file is “ped”.
Note:
remove all the empty lines at the
end of the file
The
map file describes the chromosomal location of each genetic marker and of the
QTL.
Each
row describes a single marker or the QTL:
The
Name field is not used in the analysis, as each marker will be referred
by its position in the chromosome or by a progressive number.
At
the QTL position you must specify the name QTL.
The
Position field specify in centimorgans (cM) each marker position in the
chromosome, according to a Haldane genetic map.
The
two fields must be separated by a single TAB.
An
example of a map with six markers separated by 5 cM and a QTL in the middle of
the map of chromosome 24:
24 mrk1 55
24 mrk2 60
24 mrk3 65
24 QTL 67.5
24 mrk4 70
24 mrk5 75
24 mrk6 80
The
default extension for a map file is “map”.