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

BMC Bioinformatics

Table 3 Summary of panels designed from real data

LD (r2 threshold)	< 0.2	< 0.4	< 0.6	< 0.8
Number of different type of markers
Number of Markers	2067	3157	4278	5754
Number of STRs	47	64	83	115
Number of SNPs	2020	3093	4195	5639
Summary of r2
Min	0.000	0.000	0.000	0.000
1st Qu	0.000	0.002	0.003	0.006
Median	0.000	0.009	0.018	0.037
Mean	0.020	0.042	0.074	0.124
3rd Qu	0.020	0.042	0.084	0.159
Max	0.990	0.991	0.991	0.991

This is the summary for panels designed out of real data. On the chromosome 22, 4 mixed panels have been generated from the SNP-STR reference haplotype panel of Gymrek’s lab [20]. The pruning was completed on plink/1.90 with threshold of pairwise correlation 0.2, 0.4, 0.6 and 0.8, with the code “--indep-pairwise”. The second part of Table 3 presents the summary of \(r^{2}\) values for each panel. The lists of \(r^{2}\) were calculated and exported with the code “ –r2 –ld-window-r2 0”.

ISSN: 1471-2105