Critical values and variation in type I error along chromosomes in the COGA dataset using the applied pseudo-trait method

Table 2 Mean of p-value distribution, summarized over all 80 pseudo-traits using 7 MB definition of chromosome ends (Affymetrix data)

	Whole genome	p term (7 MB)^b	Mid-chromosome	q term deciles^c
Haseman-Elston
mean	0.503	0.502	0.503	0.506
SD	0.018	0.035	0.019	0.037
No. SNPs^a	9857–10803	383–437	9059–9968	330–386
ROMP-one
mean	0.496	0.494	0.496	0.498
SD	0.015	0.023	0.015	0.020
No. SNPs^a	9817–10802	380–436	9023–9968	330–386
ROMP/ROOP-one
mean	0.487	0.485	0.487	0.488
SD	0.021	0.028	0.021	0.026
No. SNPs^a	9769–10802	380–436	9016–9968	330–386
ROMP-all
mean	0.479	0.479	0.478	0.483
SD	0.032	0.035	0.032	0.034
No. SNPs^a	9845–10807	381–437	9051–9972	330–386
ROMP/ROOP-all
mean	0.456	0.453	0.456	0.459
SD	0.034	0.042	0.034	0.035
No. SNPs^a	9825–10807	381–437	9030–9972	330–386

^aThe number of SNPs varies due to missing data and variable numbers of markers excluded by synteny.
^bThe p ends of chromosomes 13, 14, 15, 19, 21, 22 could not be used.
^cThe q ends of chromosomes 9, 16, 17 could not be used.

ISSN: 2730-6844