A posteriori binary cluster analyses (linkage between groups, phi-4-point correlation) were calculated to facilitate the categorization of these MiL areas.
Analagous to RH data representing presence or absence of a marker in a cell line, binary representation of linkage data indicates presence or absence of a maternal allele on an individual chromosome.
Accounting for sequence divergence and recombination rate revealed an overall weak yet statistically significant association between autosomal linkage and increased polymorphism (Kendall's partial τ = -0.17, P = 0.02, where chromosomal location is coded as a binary metric with autosomal linkage = 0 and X-linkage = 1).
Regulatory themes within exCs were visualised using hierarchical clustering of robust, annotated motifs using binary distance and average linkage.
The script to order markers on the integrated map starts by merging the binary backcross representation of linkage data with the haploid model RH data, assuming common marker order (dsmergor).
To represent the dominant allelic series, the Tabby alleles were coded as binary factors for the linkage analysis: 111 representing T a, 011 representing T m and 001 representing the t b allele.
For Chromosome 8, the regression tree for marker D8S516 (Figure 4c) at the original "Hindu" peak of linkage showed that the primary binary decision for families contributing to linkage at this marker was determined by whether they lived east or west of the UTM easting 323,564 m.
For Chromosome 6, the regression tree for marker D6S244 (Figure 4a) at the original "Hindu" peak of linkage showed that the primary binary decision for families contributing to linkage at this marker was determined by whether they lived north or south of the UTM northing 2,886,078 m.
First, unlike in plant and animal asexuals, the 180 macronuclear chromosomes do not function as a single, fixed linkage group during binary fission.
Since all the affected individuals defined by the four binary subphenotypes had ASD, the linkage analyses were for both the subphenotypes and ASD using a subset of families that met the criteria.
