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lm_auto
parameter file
Here is an annotated parameter file `par15a' for lm_auto
:
input pedigree file 'ped15' input seed file 'seed15' |
These statements are already familiar. The pedigree file given, `ped15', is the JV pedigree where the final individual is affected for a rare recessive trait (allele frequency 0.05). See Thompson (2000) Section 10.4.
The seed file contains one or more `set sampler seeds' statements to set the random seeds.
select all markers traits 1 |
There are five markers and one trait locus. This is similar to the `simulate' statement (see genedrop computing requests).
map gender F markers recomb fracts .2 .2 .2 .2 map gender M markers recomb fracts .1 .3 .1 .3 map gender F trait 1 marker 2 recomb fract .1127 map gender M trait 1 marker 2 recomb fract .055 |
The `map' statements specify the marker map and trait position in terms of recombination fractions. In this example there are five markers with gender--specific maps. The trait locus is between markers 2 and 3, with recombination fractions given in terms of the marker to its left (2). See genedrop mapping model parameters.
set markers 1 2 3 4 5 freqs .2 .2 .4 .2 set trait 1 freqs .95 .05 |
The markers all have four alleles (labeled 1--4) with frequencies 0.2, 0.2, 0.4, and 0.2. The trait has a rare allele with frequency 0.05. See genedrop population model parameters.
set marker data 5 333 1 3 1 3 1 3 1 3 1 3 331 3 4 3 4 3 4 3 4 3 4 334 2 3 2 3 2 3 2 3 2 3 431 3 4 3 4 3 4 3 4 3 4 531 3 3 3 3 3 3 3 3 3 3 |
This sets the marker data for typed individuals (can also be given in a separate file specified in `input marker data file' statement). The number of markers, 5, follows `set marker data'.
The trait data are actually given in the pedigree file. Here trait number is 1, which defaults to the first integer after the "regular" items (names and gender).
The default trait type is genotypic. Trait data are given as coded genotypes: 1 = homozygous for the first allele (with respect to the order in the allele frequency statement); 3 = heterozygous; 4 = homozygous for the second allele; 0 = unobserved. Since the trait genotypes are not observed, they are postulated from the phenotypes by assuming a recessive model. In this pedigree file `ped15', the genotype of affected individual 531 is 4 (the second allele being the rare disease allele) while the others all are 0.
set proband gametes 531 1 531 0 331 0 333 1 |
The `set proband gametes ...' is the key statement of
lm_auto
. It specifies for which haplotypes to score ibd
probabilities. After the statement keywords, a list of individual IDs
and an indicator of paternal (1) or maternal (0) haplotype is given.
For example, `531 1' means the paternal (1) haplotype of 531.
The example statement requests scoring both haplotypes of 531, the maternal(0) haplotypes of 331 and the paternal (1) haplotype of 333. See ibddrop statements, for the key statement `set proband gametes'.
set window patterns 0 4 set locus window 3 |
This example includes a pair of statements to jointly score ibd patterns for a moving window over adjacent loci. The first statement selects the ibd states to be scored, the second specifies the size of the moving window. This will make more sense when we look at the output from the example.
set L-sampler probability 0.2 set MC iterations 2000 |
This specifies 2000 sampling iterations, using the L-sampler 20 percent
of the time (using the M-sampler otherwise). These iterations are preceded
by burn-in iterations; lm_auto
uses a default of 10 percent of
the number of main iterations for burn-in. In practice, one would run the
MCMC sampler much longer than 2000 iterations. This is just for
demonstration.
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