<rnb.xml>
	<assembly>hg19</assembly>
	<region.types>tiling1kb,cpgislands,genes,promoters,51Hf0xBlxxCt.cssv1.20151105.enhmrg,ensembleRegBuildBPall,ensembleRegBuildBPctcf,ensembleRegBuildBPdistal,ensembleRegBuildBPdnase,ensembleRegBuildBPproximal,ensembleRegBuildBPtfbs,ensembleRegBuildBPtss</region.types>
	<identifiers.column>sampleId</identifiers.column>
	<colors.category>#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666,#2166AC,#B2182B,#00441B,#40004B,#053061</colors.category>
	<colors.meth>#EDF8B1,#41B6C4,#081D58</colors.meth>
	<min.group.size>1</min.group.size>
	<max.group.count>12</max.group.count>
	<import.table.separator>\t</import.table.separator>
	<import.bed.style>BisSNP</import.bed.style>
	<qc.coverage.plots>false</qc.coverage.plots>
	<filtering.sex.chromosomes.removal>false</filtering.sex.chromosomes.removal>
	<filtering.missing.value.quantile>0.6</filtering.missing.value.quantile>
	<filtering.coverage.threshold>5</filtering.coverage.threshold>
	<filtering.low.coverage.masking>true</filtering.low.coverage.masking>
	<filtering.high.coverage.outliers>true</filtering.high.coverage.outliers>
	<filtering.greedycut>false</filtering.greedycut>
	<exploratory.columns>cellType,technology,individual</exploratory.columns>
	<exploratory.intersample>false</exploratory.intersample>
	<exploratory.clustering.heatmaps.pdf>true</exploratory.clustering.heatmaps.pdf>
	<exploratory.region.profiles>genes</exploratory.region.profiles>
	<exploratory.gene.symbols>CCR5,CSF2,GAS5,ZFAS1,RUNX1,RUNX3,ANPEP,CD22,CD28,CD34,CD36,ITGAM,ITGAV,PECAM1,THPO,FAS,IFNGR1,IRF6,JMJD6</exploratory.gene.symbols>
	<differential.site.test.method>limma</differential.site.test.method>
	<differential.comparison.columns>cmp_TCMvsTN,cmp_TEMvsTCM,cmp_TEMvsTN,cmp_TCMvsTN_WGBS,cmp_TEMvsTCM_WGBS,cmp_TEMvsTN_WGBS,cmp_TCMvsTN_NOMe,cmp_TEMvsTCM_NOMe,cmp_TEMvsTN_NOMe,cmp_tech_TCM,cmp_tech_TEM,cmp_tech_TN,cmp_individual</differential.comparison.columns>
	<columns.pairing names="cmp_tech_TCM,cmp_tech_TEM,cmp_tech_TN">individual,individual,individual</columns.pairing>
	<differential.enrichment>true</differential.enrichment>
	<replicate.id.column>cellType</replicate.id.column>
	<export.to.trackhub>bigBed</export.to.trackhub>
	<logging.memory>true</logging.memory>
	<logging.disk>true</logging.disk>
	<disk.dump.big.matrices>true</disk.dump.big.matrices>
	<enforce.memory.management>true</enforce.memory.management>
	<gz.large.files>true</gz.large.files>
</rnb.xml>
