<rnb.xml>
	<analysis.name>Ewing Sarcoma</analysis.name>
	<logging>true</logging>
	<data.source>data,data/sample_annotation.csv,filename</data.source>
	<dir.reports>reports</dir.reports>
	<data.type>bed.dir</data.type>
	<assembly>hg38</assembly>
	<columns.pairing null="null"></columns.pairing>
	<analyze.sites>true</analyze.sites>
	<region.types>tiling1kb,tiling200bp,genes,promoters,cpgislands,ensembleRegBuildBPall</region.types>
	<region.aggregation>mean</region.aggregation>
	<region.subsegments>0</region.subsegments>
	<preanalysis.script>preanalysis.R</preanalysis.script>
	<region.subsegments.types null="null"></region.subsegments.types>
	<identifiers.column>sample_id</identifiers.column>
	<colors.category>#1B9E77,#D95F02,#7570B3,#E7298A,#66A61E,#E6AB02,#A6761D,#666666</colors.category>
	<colors.gradient>#132B43,#56B1F7</colors.gradient>
	<min.group.size>2</min.group.size>
	<max.group.count null="null"></max.group.count>
	<gz.large.files>true</gz.large.files>
	<import>true</import>
	<import.default.data.type>bed.dir</import.default.data.type>
	<import.table.separator>,</import.table.separator>
	<import.bed.style>EPP</import.bed.style>
	<import.bed.frame.shift>1</import.bed.frame.shift>
	<import.bed.test>true</import.bed.test>
	<import.bed.test.only>false</import.bed.test.only>
	<import.skip.object.check>false</import.skip.object.check>
	<import.gender.prediction>true</import.gender.prediction>
	<qc>true</qc>
	<qc.boxplots>true</qc.boxplots>
	<qc.barplots>true</qc.barplots>
	<qc.negative.boxplot>true</qc.negative.boxplot>
	<qc.snp.heatmap>true</qc.snp.heatmap>
	<qc.snp.distances>true</qc.snp.distances>
	<qc.snp.boxplot>false</qc.snp.boxplot>
	<qc.snp.barplot>false</qc.snp.barplot>
	<qc.coverage.plots>false</qc.coverage.plots>
	<qc.coverage.threshold.plot>1,2,3,4,5,6,7,8,9,10</qc.coverage.threshold.plot>
	<qc.coverage.histograms>true</qc.coverage.histograms>
	<qc.coverage.violins>true</qc.coverage.violins>
	<qc.sample.batch.size>500</qc.sample.batch.size>
	<preprocessing>true</preprocessing>
	<normalization>false</normalization>
	<normalization.method>none</normalization.method>
	<normalization.background.method>none</normalization.background.method>
	<normalization.plot.shifts>true</normalization.plot.shifts>
	<filtering.whitelist null="null"></filtering.whitelist>
	<filtering.context.removal>CC,CAG,CAH,CTG,CTH,Other</filtering.context.removal>
	<filtering.snp>3</filtering.snp>
	<filtering.cross.reactive>false</filtering.cross.reactive>
	<filtering.greedycut>false</filtering.greedycut>
	<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.deviation.threshold>0</filtering.deviation.threshold>
	<imputation.method>none</imputation.method>
	<inference>true</inference>
	<inference.age.column>patient_age</inference.age.column>
	<inference.age.prediction>true</inference.age.prediction>
	<inference.age.prediction.training>false</inference.age.prediction.training>
	<inference.age.prediction.predictor null="null"></inference.age.prediction.predictor>
	<inference.age.prediction.cv>false</inference.age.prediction.cv>
	<exploratory>true</exploratory>
	<exploratory.columns>disease_type,disease_type_detailed,sample_source,tumor_location,tumor_size,relapse,metastases_at_diagnosis,comp.column,Tissue_vs_MSC</exploratory.columns>
	<exploratory.top.dimensions>0</exploratory.top.dimensions>
	<exploratory.principal.components>5</exploratory.principal.components>
	<exploratory.correlation.pvalue.threshold>0.01</exploratory.correlation.pvalue.threshold>
	<exploratory.correlation.permutations>10000</exploratory.correlation.permutations>
	<exploratory.correlation.qc>true</exploratory.correlation.qc>
	<exploratory.beta.distribution>true</exploratory.beta.distribution>
	<exploratory.intersample>true</exploratory.intersample>
	<exploratory.deviation.plots null="null"></exploratory.deviation.plots>
	<exploratory.clustering>top</exploratory.clustering>
	<exploratory.clustering.top.sites>1000</exploratory.clustering.top.sites>
	<exploratory.clustering.heatmaps.pdf>false</exploratory.clustering.heatmaps.pdf>
	<exploratory.region.profiles>genes,promoters,cpgislands</exploratory.region.profiles>
	<exploratory.gene.symbols>CXCL8,EMILIN1,C20orf141</exploratory.gene.symbols>
	<exploratory.custom.loci.bed null="null"></exploratory.custom.loci.bed>
	<differential>true</differential>
	<differential.site.test.method>limma</differential.site.test.method>
	<differential.permutations>0</differential.permutations>
	<differential.comparison.columns>disease_type,disease_type_detailed,sample_source,tumor_location,tumor_size,relapse,metastases_at_diagnosis,comp.column,Tissue_vs_MSC</differential.comparison.columns>
	<differential.comparison.columns.all.pairwise null="null"></differential.comparison.columns.all.pairwise>
	<covariate.adjustment.columns null="null"></covariate.adjustment.columns>
	<differential.adjustment.sva>true</differential.adjustment.sva>
	<differential.variability>true</differential.variability>
	<differential.variability.method>diffVar</differential.variability.method>
	<differential.enrichment.go>true</differential.enrichment.go>
	<differential.enrichment.lola>true</differential.enrichment.lola>
	<differential.report.sites>true</differential.report.sites>
	<export.to.bed>false</export.to.bed>
	<export.to.trackhub>bigBed,bigWig</export.to.trackhub>
	<export.to.csv>false</export.to.csv>
	<export.to.ewasher>false</export.to.ewasher>
	<export.types>sites</export.types>
	<colors.meth>#AD0021,#909090,#39278C</colors.meth>
	<colors.3.gradient>#832424,#FFFFFF,#3A3A98</colors.3.gradient>
	<logging.memory>true</logging.memory>
	<logging.disk>true</logging.disk>
	<logging.exit.on.error>false</logging.exit.on.error>
	<distribution.subsample>1000000</distribution.subsample>
	<disk.dump.big.matrices>true</disk.dump.big.matrices>
	<disk.dump.bigff>true</disk.dump.bigff>
	<disk.dump.bigff.finalizer>delete</disk.dump.bigff.finalizer>
	<enforce.memory.management>false</enforce.memory.management>
	<enforce.destroy.disk.dumps>true</enforce.destroy.disk.dumps>
</rnb.xml>
