ROC analysis yielded AUC values of 0.9 for UE visual scoring, 0.86 for strain scoring and 0.82 for CU.
Using cut-off points for biopsy selected for the study, sensitivity was 90% for UE visual scoring, 100% for strain scoring and 76% for CU.
First, Pearson's correlations were calculated for phenotypic correlations (calculated using individual values) and approximate genetic correlations (calculated using the mean score for each strain) in all consomic strains and B6 (Blizard & Bailey 1979; Crusio 2007).
For WASF, the final fused score (FS) for strain i will be: F S i = ∑ j (P A T i, j * W j ) When WBF is used for strain i and pathway j, B i, j is the sum of strains with lower PAT than strain i.
For each divergent region (Table S3), we then plotted the placement score for each strain against the two genomes.
The phenotypic characteristics data are depicted in Table 2 and the Additional file 1: Table S1 as final scores for each strain and stress condition, ranging between 0 (no growth) and 8 (active growth).
For all putative polymorphic loci, GigaBayes first computes the posterior likelihood of the three mostly likely diploid genotypes for each aligned strain based on the observed alleles and quality scores for that strain.
The transferred pathway activity score (PAT) generated for strain i and pathway j is calculated as follows: P A T i, j = 1 − | E j − P A N i, j | Another important parameter, weight (W), is to characterize the relative importance of a particular pathway compared with other pathways in aggregation.
As the viral fitness measured in this study was relative to that of the pathogenic reference strain HIV-1MBC925, fitnescoresres for test strains were calculated relative to HIV-1 DNA production by HIV-1MBC925 from coincident time points.
Many sites followed a simple binary pattern, with scores for each strain against N2 and CB4856 resembling one of the controls.
