6.3 Sample markerdrop parameter file -- conditional on inheritance pattern

The sample parameter file, `ped73_mdrop_inhe.par', requests simulation of marker data conditional on an inheritance pattern. The relevant section of the file is:

map trait 3 marker 4 recomb frac 0.01 simulate markers 10 using inheritance map marker positions 10 20 30 40 50 60 70 80 90 100 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 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 4 with a recombination fraction of 0.01. The `simulate markers 10 using inheritance' statement indicates the number of markers to be simulated and specifies that the markers will be conditional on the inheritance pattern. The `map marker positions' statement specifies the spacing of the markers to be simulated. The `map marker positions' statements beginning at line 4 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 the marker data.

The parameter file `ped73_mdrop_inhe.par' uses pedigree file `ped73.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 4 *************************************************** 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 -1 999.5 301 201 2010 1 0 0 0 1 1 999.5

The first three columns are indices of individuals and their parents. The next two are sex and observation status. The last two integer columns are inheritance indicators with the first being the paternal ones and the second the maternal ones. A founder's inheritance indicators are `-1 -1'.

The connection to these inheritance data is through the statement

input pedigree record trait 3 integer pair 5 6

in the parameter file. Recall that on counting the pedigree file columns the integers follow the three names, so that integers 5 and 6 are indeed the last two integer columns in this pedigree file.

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

For more information on markerdrop options see markerdrop statements.