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 are required for markerdrop and must be included in the parameter file. 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 are simulating data. In this example, the trait locus follows marker 5 at a distance of 5 centiMorgans. The `simulate markers 10 using trait' statement indicates the number of markers to be simulated and specifies that the markers will be conditional on a trait model. The `map marker positions' statement specifies the spacing of the markers to be simulated.

Note that the parameter file for running a simulation conditional on a trait model requires two more lines than the parameter file for simulation conditional on an inheritance pattern (see next section). These two additional lines (lines 4 and 5) are required for discrete traits (the default for simulation on a trait). Line 4: `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. Line 5: `set trait ... freqs' specifies trait allele frequencies.

The `set markers' statements beginning at line 6 must be included; they specify allele frequencies at the first two markers.

Following the `set markers 10 data' statement, the marker data availability is specified for each of the two associated alleles. A '0' indicates the data is unobserved, while a '1' indicates the data is observed. This translates into a specification of which alleles are to be used in simulating marker data.

The parameter file `ped73_mdrop_trait.par' uses the pedigree file `ped73.ped', which is found in the `MORGAN_Examples' directory. The file format section and first few lines of the pedigree data section of this file are below.

input pedigree size 73 input pedigree record names 3 integers 6 reals 1 *************************************************** 101 0 0 1 0 0 0 -1 -1 999.5 102 0 0 2 0 0 0 -1 -1 999.5 201 101 102 1 0 0 0 0 1 999.5 202 101 102 2 0 0 0 1 1 999.5 2010 0 0 2 0 0 0 -1 -1 999.5

The first three columns are indices are 'names' which are character strings. They are unique identifiers of each individual and his/her parents. By default, the parent order is father followed by mother. The next four columns are sex (1=male, 2=female), observed status (0=unobserved, 1=observed) and affection status for two possible discrete traits (0=missing, 1=unaffected, 2=affected). The affection status is to be used is specified through statements in the parameter file:

input pedigree record trait 2 integer 4

This statement specifies that "trait 2" is the fourth integer in the pedigree file, after the three names (that is, the 7 th item). Traits may be given any integer label: here "2" is an arbitrary choice.

If desired, this statement can be included in the pedigree file instead. Other columns is the pedigree file are explained in the next section.

Note that markerdrop can simulate data for markers linked to only one trait locus, as specified in the `map' statement in the parameter file.