question about columns in output file

[karens99]

When I run my gene-based SKAT analyses, I get the following output file:

#GROUPNAME | NUM_VAR | VARs | AVG_AF | MIN_AF | MAX_AF | STATISTICS | PVALUE_DAVIES | PVALUE_LIU
AKR1C3 | 715 |   | 0.001356 | 0.000542 | 0.010907 | 3.08E+07 | 0.219887 | 0.221904
ALOX5 | 963 |   | 0.00144 | 0.000542 | 0.010463 | 4.54E+07 | 0.196564 | 0.201288
AS3MT | 347 |   | 0.001289 | 0.000542 | 0.010591 | 1.40E+07 | 0.316914 | 0.318118

My question is, what is the column called STATISTICS? The values seem to be quite large, and I have been unable to find an explanation of what this column contains. Thanks!

[welchr]

I believe that's the SKAT test statistic Q, written out here:

https://genome.sph.umich.edu/wiki/RAREMETAL_METHOD#SKAT_META_ANALYSIS

Appears here in the code:

raremetal/raremetal/src/Meta.cpp

Lines 3892 to 3899 in 2c82cfc

	if (fullResult)
	{
	ifprintf(output,
	"#GROUPNAME\tNUM_VAR\tVARs\tMAFs\tSINGLEVAR_EFFECTs\tSINGLEVAR_PVALUEs\tAVG_AF\tMIN_AF\tMAX_AF\tSTATISTICS\tPVALUE_DAVIES\tPVALUE_LIU\n");
	} else
	{
	ifprintf(output, "#GROUPNAME\tNUM_VAR\tVARs\tAVG_AF\tMIN_AF\tMAX_AF\tSTATISTICS\tPVALUE_DAVIES\tPVALUE_LIU\n");
	}