Sib-pair Command: neff

Class	Analysis and data manipulation command
Name	neff
Arguments	[<map_window_width> [<critical_P_value>

Calculates the effective number of association tests using the set of active (autosomal) markers, allowing for the observed intermarker linkage disequilibrium. Implements the approach of Moskvina & Schmidt [2008], which needs the maximum (Pearson) intermarker r for each locus in turn with all preceding loci as one moves along the chromosome (down the map).

The optional parameters are the width of the sliding map window containing markers to be tested versus the current iterated marker (currently 1 cM or 1 Mbp), and the genome-wide critical P-value (defaults to 0.05).

Example:

>> set ple 2

NOTE:  Print level  2

>> neff

Marker          max r  Neff
--------------- ------ ----------
T-5491C         -.1544       1.0
A-5466C         0.9897       1.0
T-3892C         0.8410       1.1
A-240T          0.9790       1.6
T-93C           1.0000       1.8
T1237C          0.7100       1.8
G2215A          0.8381       2.5
ACE_ID          0.9999       3.0
G2350A          0.9952       3.0
4656CT          0.9550       3.1

Effective number of tests =       3.4 (  33.7%)
Equivalent critical alpha = .151242293E-01

References

Moskvina V, Schmidt KM (2008). On multiple-testing correction in genome-wide association studies. Genet Epidemiol 32: 567-573.

See also:

dis	intragametic association