Input Files
GRR requires a single pedigree file as input in free format.
Each line describes a single individual, and includes a family
identifier, a personal identifier, paternal and maternal identifiers
and a sex code (1 for males, 2 for females). These are followed
by genotypes and phenotypes. GRR provides the option of deleting the first
N columns following the mandatory first five columns and deleting the last N
columns. Typically phenotypic data will appear before or after the marker
data (not in between) and GRR allows for its removal, since the program makes no
use of phenotypes.
Marker genotypes are encoded as two consecutive integers and
missing values can be encoded as zeros (0) or exes (x). Marker
genotypes may be encoded as an allele pair
separated by a forward-slash (/), but the slash is optional.
Further information on the format of the input file can be obtained
from the QTDT website.
We begin by loading the pedigree file into the program. There are only
two options once a file is selected. The first is that pairings of
individuals can be made within families only or across all pairs of
individuals. Be warned, using all pairs on a big sample can take well over
a minute to process. For our example, however, we will use the
timeconsuming but valuable option of all pairs.
The second option is to select how many columns to skip in the datafile, if
any. Columns after the first 5 mandatory columns may be skipped and
columns at the end may be skipped. For our example, sample.ped contains
only marker data, so no columns need to be skipped.
Let's look for pedigree errors now!
| 
