9.6.7 Autozyg computational parameters

• See ibddrop statements, for statements specifying the proband gametes and locus window for lm_auto.

• See ibddrop statements, for the statement for setting the seeds for the LM-sampler.

set [chromosome I] markers K data N1 M11 M12 ... [N2 M21 M22 ...] ...

Individuals with at least one observed marker are named, together with their marker genotypes. The number of allele pairs for an individual is the same as the number of markers mapped on the chromosome. Marker loci not observed for an individual are given alleles `0 0'. (Those individuals with no observed markers need not be included in this statement.) In the example, there are 5 markers mapped for the chromosome:

set markers 5 data 343 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 4 3 3 0 0 3 3 3 3

set [component M] [scoreset N] proband gametes N1 K1 N2 K2...

This statement is required for lm_auto. One or more scoring sets may be given for each pedigree component, where a scoring set consists of two or more haplotypes. If there is more than one set for the component, each set is assigned a number 1 or greater. The maximum number of haplotypes in each set is limited to 10, due to computer memory considerations.

Pairs of names and meiosis indicators are given, with 0 indicating maternal inheritance and 1 indicating paternal inheritance. In the example, there are two sets for the component:

set component 1 scoreset 2 proband gametes 531 1 531 0 331 0 331 1 set component 1 scoreset 4 proband gametes 561 1 362 0 364 1

At least one proband gamete set must be specified when running lm_auto.

set [chromosome I] locus window K

This statement is optional for lm_auto and gives the window size (number of loci) for which the multi-locus ibd probabilities are scored. If no size is given, each locus is scored separately.

set [component M] [scoreset N] window patterns L1...

This statement is a companion to `set locus window' and is required for lm_auto when the window option is chosen. It identifies the ibd patterns to be jointly scored for the proband gamete set N assigned by the `set proband gametes' statement. A prior run, with the same proband gametes, but without the window option is needed to select the ibd patterns. That is, the user is required to list ibd patterns of interest by label; the labeling of the patterns is not obvious without first running lm_auto. In the example, we were interested in ibd patterns `1 1 1 1' and `1 1 2 2', which are assigned labels `0' and `4', respectively, in the output table headed `Probabilities of IBD patterns'. One needs to run lm_auto to obtain these labels.

set trait data (genotypic | discrete | quantitative)

Trait data are specified as genotypic, discrete (phenotypic), or quantitative (continuous). With a genotypic trait, the trait locus genotype can be inferred from the trait value. There are four possible trait values: `0' = missing, `1' = homozygous for allele 1, `3' = heterozygous, and `4' = homozygous for allele 2. There are three possible trait values with a discrete (or phenotypic trait): `0' = missing, `1' = unaffected, and `2' = affected. If a discrete trait is chosen, the next statement, `set incomplete penetrances', must be included. With a quantitative trait, a missing value is denoted as a real number with integer portion `999'. For example, `999', `999.3' and `999.543' all mean `missing'. The default trait type is genotypic.

set incomplete penetrances X1 X2 X3

This statement is required for discrete trait data. Penetrances (probability of expressing the trait) are provided for the (1 1), the (1 2), and the (2 2) genotypes, respectively.

set [component M] affected individuals N1 N2 ...

lm_pval needs to know which members of the pedigree are affected with the disease: there are two ways to specify this. Affected individuals (for at least one component) may be named in this statement. Or, use the following statement if the affected individuals are to be determined from the pedigree data file.

set affected individuals trait K

Here, lm_pval is to determine the affected individuals from the trait data in the pedigree file. A trait genotypic code of 3 (genotype (1 2) or (2 1)) or 4 (genotype (2 2)) indicates an affected individual. The trait number, K, determines the position of this genotypic code in the pedigree records (see Pedigree file description statements).