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

Table 1 Mean of p-value distribution, summarized over all 80 pseudo-traits using decile definitions (Affymetrix data)

	Whole genome	p term deciles^b	Mid-chromosome	q term deciles
Haseman-Elston
mean	0.503	0.499	0.503	0.506
SD	0.018	0.032	0.021	0.032
No. SNPs^a	9857–10803	842–969	7936–8691	993–1129
ROMP-one
mean	0.496	0.496	0.496	0.498
SD	0.015	0.020	0.015	0.017
No. SNPs^a	9817–10802	834–968	7896–8691	984–1129
ROMP/ROOP-one
mean	0.487	0.487	0.487	0.488
SD	0.021	023	0.022	0.022
No. SNPs^a	9769–10802	832–968	7861–8691	984–1129
ROMP-all
mean	0.479	0.479	0.478	0.483
SD	0.032	0.033	0.032	0.031
No. SNPs^a	9845–10807	839–969	7925–8695	989–1129
ROMP/ROOP-all
mean	0.456	0.455	0.456	0.458
SD	0.034	0.036	0.034	0.033
No. #SNPs^a	9825–10807	837–969	7910–8695	989–1129

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

ISSN: 2730-6844