<rnb.xml>
	<analysis.name>Dynamic DNA Methylation Landscape</analysis.name>
	<data.source>data,data/samples.csv</data.source>
	<dir.reports>reports</dir.reports>
	<data.type>bed.dir</data.type>
	<assembly>hg19</assembly>
	<region.types>tiling,genes,promoters,cpgislands</region.types>
	<identifiers.column>Sample_name</identifiers.column>
	<colors.category>#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666,#2166AC,#B2182B</colors.category>
	<min.group.size>1</min.group.size>
	<max.group.count>20</max.group.count>
	<import.bed.style>EPP</import.bed.style>
	<qc.coverage.plots>false</qc.coverage.plots>
	<filtering.sex.chromosomes.removal>true</filtering.sex.chromosomes.removal>
	<filtering.missing.value.quantile>0.5</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>sampleGroup_short,Source,sample_class,sample_cohort,organ,germ_layer</exploratory.columns>
	<exploratory.intersample>false</exploratory.intersample>
	<exploratory.region.profiles>genes,promoters</exploratory.region.profiles>
	<differential.site.test.method>limma</differential.site.test.method>
	<differential.comparison.columns>cmp_ESC_vs_differentiated,cmp_colon_tumor_vs_normal,cmp_brain_AD_vs_normal</differential.comparison.columns>
	<differential.enrichment>true</differential.enrichment>
	<export.to.trackhub>bigBed</export.to.trackhub>
	<logging.memory>true</logging.memory>
	<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>
