<?xml version="1.0" encoding="utf-8" ?>
	
<settings>
	<defaults>
	
		<qc>
			<snpqccallratethreshold>0.95</snpqccallratethreshold> 		<!-- Double:	[0-1] call rate threshold used for snp qc -->
			<snpqchwethreshold>0.0001</snpqchwethreshold>				<!-- Double:	[0-1] hardy-weinberg threshold used for snp qc -->
			<snpqcmafthreshold>0.05</snpqcmafthreshold>					<!-- Double:	[0-1] minor allele frequency threshold used for snp qc -->
		</qc>

		<analysis>
			<analysistype>cis</analysistype>							<!-- String:	[cis/trans/cistrans] perform cis-only, trans-only, or cis+trans analysis -->
			<cisanalysisprobedistance>250000</cisanalysisprobedistance>	<!-- Integer:	[0-R) probe distance used to qualify a probe/cis combination as cis -->
			<threads>1</threads>										<!-- Integer: 	[1-R) Number of threads to use during calculation. If threads > number processors || threads < 1, threads is replaced by nr of processors -->
		</analysis>

		<multipletesting>
			<type>fdr</type>											<!-- String:	[fdr] multiple testing correction to use -->
			<threshold>0.05</threshold>									<!-- Double:	[0-1] threshold for multiple testing procedure -->
			<permutations>0</permutations>								<!-- Integer:	[0-R) number of permutations to perform -->
		</multipletesting>

		<output>
			<outputdirectory>/Data/BenchMark/MetaQTL2-Lude-VectorMergeFix-8thread/</outputdirectory>				<!-- String:	directory to output results -->
			<outputplotthreshold>1e-24</outputplotthreshold>			<!-- Double:	[0-R) threshold for generating eQTL plots -->
			<outputplotdirectory>/Data/BenchMark/MetaQTL2-Lude-VectorMergeFix-8thread/plots/</outputplotdirectory>	<!-- Integer:	directory to output plots. When left blank, <outputdirectory> is used -->
			<maxnreqtlresults>150000</maxnreqtlresults>
		</output>

		<confine>
			<snp></snp>									<!-- String:	location of file containing the subset of SNP to be tested -->
			<probe></probe>							<!-- String:	location of file containing the subset of probes to be tested -->
			<snpProbe></snpProbe>					<!-- String:	location of file containing the subset of SNP-probe combinations to be tested -->
			<confineSNPsToSNPsPresentInAllDatasets>false</confineSNPsToSNPsPresentInAllDatasets>	<!-- Boolean:	[true/false] should the analysis be confined to SNP present in all datasets? -->
			<confineToSNPsThatMapToChromosome>-1</confineToSNPsThatMapToChromosome>					<!-- Integer:	[0-R) only include SNP in the analysis that are on this chromosome. Leave blank or set to -1 to disable. -->
			<confineProbesThatMapToKnownChromosome>false</confineProbesThatMapToKnownChromosome>
		</confine>
	</defaults>

	<datasets>
	
		<dataset>
			<name></name>
			<location></location>			
			<genometoexpressioncoupling></genometoexpressioncoupling>			
			<expressiondata></expressiondata>			
			<quantilenormalize>false</quantilenormalize>			
			<logtranform>false</logtranform>		
		</dataset>
				-->	
	</datasets>
</settings>

