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

Song, Bing; Woerner, August E.; Planz, John

doi:10.1186/s12859-020-03945-0

BMC Bioinformatics

Table 2 Proportion of p values < 0.05 in 1000 times for different levels of linkage using summary statistics (only “Bias = Both” is shown, more details in Additional file 14: Table S7)

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

X.1	Panel size	Number of linked markers	Linkage	Bias	Total number of heterozygous loci (K)	Total number of shared alleles (X)
1	10	0	Unlinked	Both	0.047	0.039
2	20	0	Unlinked	Both	0.05	0.036
3	30	0	Unlinked	Both	0.051	0.048
4	40	0	Unlinked	Both	0.055	0.038
5	50	0	Unlinked	Both	0.045	0.053
6	100	0	Unlinked	Both	0.047	0.051
31	16	2	HalfQuarter-Linked	Both	0.045	0.044
32	32	4	HalfQuarter-Linked	Both	0.069	0.041
33	48	6	HalfQuarter-Linked	Both	0.072	0.063
34	64	8	HalfQuarter-Linked	Both	0.082	0.065
35	80	10	HalfQuarter-Linked	Both	0.094	0.068
36	96	12	HalfQuarter-Linked	Both	0.109	0.069
53	8	2	Quarter-Linked	Both	0.015	0.047
54	16	4	Quarter-Linked	Both	0.03	0.058
55	24	6	Quarter-Linked	Both	0.057	0.074
56	32	8	Quarter-Linked	Both	0.052	0.094
57	40	10	Quarter-Linked	Both	0.186	0.09
58	64	16	Quarter-Linked	Both	0.303	0.137
59	80	20	Quarter-Linked	Both	0.382	0.154
60	96	24	Quarter-Linked	Both	0.421	0.209
81	8	4	Half-Linked	Both	0.011	0.116
82	12	6	Half-Linked	Both	0.29	0.15
83	16	8	Half-Linked	Both	0.326	0.171
84	20	10	Half-Linked	Both	0.388	0.221
85	24	12	Half-Linked	Both	0.419	0.242
86	32	16	Half-Linked	Both	0.513	0.297
87	40	20	Half-Linked	Both	0.638	0.374
88	60	30	Half-Linked	Both	0.83	0.516
89	80	40	Half-Linked	Both	0.934	0.687
90	100	50	Half-Linked	Both	0.982	0.819
105	16	12	ThreeQuarter-Linked	Both	0.582	0.372
106	24	18	ThreeQuarter-Linked	Both	0.738	0.499
107	32	24	ThreeQuarter-Linked	Both	0.845	0.635
108	40	30	ThreeQuarter-Linked	Both	0.914	0.719
109	64	48	ThreeQuarter-Linked	Both	0.986	0.943
110	80	60	ThreeQuarter-Linked	Both	0.997	0.974
111	96	72	ThreeQuarter-Linked	Both	0.999	0.995
124	10	10	Fully-Linked	Both	0.604	0.404
125	20	20	Fully-Linked	Both	0.835	0.691
126	30	30	Fully-Linked	Both	0.957	0.849
127	40	40	Fully-Linked	Both	0.989	0.936
128	50	50	Fully-Linked	Both	0.997	0.973
129	100	100	Fully-Linked	Both	1	1

For both number of heterozygous loci and number of shared alleles, the proportions of detecting dependency in unlinked dataset are approximately less than 5%; in fully linked dataset, is over 70% when the number of markers is larger than 10. When the percentage of linked markers increases, the power of test increases

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