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Table 1 The rules of panel design for power test of simulation

From: mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

Panel size Number of linked markers Number of linked SNPs Number of linked STRs Linkage Bias
x 0 0 0 Unlinked Both
x 2 2 0 OnePair-Linked SNP
x 2 0 2 OnePair-Linked STR
x 0.125x 0.125x 0 HalfQuarter-Linked SNP
x 0.125x 0 0.125x HalfQuarter-Linked STR
x 0.125x 0.0625x 0.0625x HalfQuarter-Linked Both
x 0.25x 0.25x 0 Quarter-Linked SNP
x 0.25x 0 0.25x Quarter-Linked STR
x 0.25x 0.125x 0.125x Quarter-Linked Both
x 0.5x 0.5x 0 Half-Linked SNP
x 0.5x 0 0.5x Half-Linked STR
x 0.5x 0.25x 0.25x Half-Linked Both
x 0.75x 0.5x 0.25x ThreeQuarter-Linked SNP
x 0.75x 0.25x 0.5x ThreeQuarter-Linked STR
x 0.75x 0.375x 0.375x ThreeQuarter-Linked Both
x x-2 0.5x 0.5x-2 Almost-Linked SNP
x x-2 0.5x-2 0.5x Almost-Linked STR
x x 0.5x 0.5x Fully-Linked Both
  1. The “PanelSize” is the number of markers in each panel and in each panel, half markers are SNPs and the other half markers are STRs. In this table to illustrate the rules of design, “PanelSize” is set to “x”
  2. The variable “Linkage” is defined as the percentage of linked markers among the total. For example, if the “PanelSize” is x, the number of linked markers is 0.5x, then the “Linkage” equals to “Half-Linked”. The “OnePair-Linked” and “Almost-Linked” have unfixed percentage of linked markers but hold the numbers of linked or unlined markers. If there are only 2 linked markers, the “Linkage” is defined as “OnePair-Linked”; if there are only 2 unlinked markers and all others are linked, the “Linkage” is defined as “Almost-Linked”
  3. The variable “Bias” is defined as the distribution of linked markers. If the number of linked SNPs is larger than linked of STRs, the “Bias” equals to “SNP”; in contrast, if the number of linked SNPs is smaller than linked STRs, the “Bias” equals to “STR”; but if the number of linked SNPs and STRs are the same, “Bias = Both”. When the linked markers are less than 50% of total markers, in the biased groups, all linked markers are the same type of markers- the biased one. When the linkage is higher than “Half-Linked”, all the biased markers are linked, and the unlinked markers are found on the other type