6.2 Sample markerdrop parameter file -- conditional on trait

Files for markerdrop may be found in the `Simulation' subdirectory of `MORGAN_Examples'. The sample parameter file, `ped73_mdrop_trait.par', requests simulation of marker data conditional on a trait model. The trait is assumed to be discrete when simulation is conditional on a trait model. The relevant section of the file is:

map trait 2 marker 5 distance 5.0 simulate markers 10 using trait map marker positions 10 20 30 40 50 60 70 80 90 100 set incomplete penetrances .05 .6 .95 set trait 2 freqs 0.5 0.5 set markers 1 freqs 0.13 0.66 0.16 0.05 set markers 2 freqs 0.06 0.23 0.41 0.25 0.05 . . . set markers 10 data 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 201 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 202 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2010 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 301 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 302 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 304 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 . . .

The first three lines of each of the parameter files above are required for markerdrop, regardless of simulation of marker data on a trait or on an inheritance pattern. The `map trait' statement identifies the trait locus to be used in the simulation and gives its position relative to the markers on which we wish to simulate data. In this example, the trait locus follows marker 5 at a distance of 5 centiMorgans. The `simulate markers 10 using trait' statement states the number of markers to be simulated and specifies simulation using a trait model. The `map marker positions' statement specifies the spacing of the markers to be simulated.

Compared with the parameter file needed for simulation conditional on inheritance pattern (see next section), `ped73_mdrop_trait.par' contains two additional lines (lines 4 and 5), which are required for discrete traits (the default for simulation on a trait). `set incomplete penetrances' specifies the probability of exhibiting the trait for individuals with trait locus genotypes `1 1', `1 2' (or `2 1') and `2 2', respectively. `set trait ... freqs' specifies trait allele frequencies.

Starting from line 6, the statements specify allele frequencies at the first two markers and are required.

Following the statement `set markers 10 data', patterns of marker data to be simulated are given for each individual. Ten markers correspond to 10 pairs of 0's or 1's, with 0's representing "unobserved" and 1's "observed".

File `ped73_mdrop_trait.par' uses pedigree file `ped73_ph.ped'. The file format section and first few lines of the pedigree data setion of this file are below.

input pedigree size 73 input pedigree record names 3 integers 3 *************************************************** 101 0 0 1 0 0 102 0 0 2 0 0 201 101 102 1 0 0 202 101 102 2 0 0 2010 0 0 2 0 0 301 201 2010 1 0 0 302 201 2010 2 1 1

The first three columns are indices of each individual and his/her parents, whereas the last three columns are sex (1=male, 2=female), observed status (0=unobserved, 1=observed) and affectation status (0=missing, 1=unaffected, 2=affected). The affectation status is actually specified through a statement in the parameter file:

input pedigree record trait 2 integer 3

This statement can be included in the pedigree file instead. But markerdrop can simulate data for markers linked to only one trait locus, as specified in the `map' statement in the parameter file.