Files in isglobal-brge/EASIER
EwAS: quality control, meta-analysIs and EnRichment
.DS_Store
.gitignore
DESCRIPTION
EASIER.Rproj
LICENSE
NAMESPACE
R/Chromatin_enrichment.R
R/MSigDB_enrichment.R
R/RcppExports.R
R/addCrom15Columns.R
R/addDhsColumns.R
R/addGroupColumns.R
R/addPhantomSummary.R
R/adjust_data.R
R/clean_NA_from_data.R
R/create_GWAMA_files.R
R/data.R
R/descriptives_CpGs.R
R/easier_package.R
R/exclude_CpGs.R
R/filterCpGs.R
R/filterLowRepresentedCpGsinCohort.R
R/findOverlapValues.R
R/generate_hapmap_file.R
R/getAllChromStateOR.R
R/getAllChromStateRegressions.R
R/getAllFisherTest.R
R/getAllHypergeometricTest.R
R/getAllRelativeIslandOR.R
R/getBinaryClassificationYesNo.R
R/getChromStateOR.R
R/getChromStateRegression.R
R/getEnrichGenomicRanges.R
R/getEntrezIdfromSymbol.R
R/getFisherTest.R
R/getHyperHypo.R
R/getHypergeometricTest.R
R/getPMDGenomicRanges.R
R/getRelativeIslandOR.R
R/getUniqueGenes.R
R/getUniqueValues.R
R/get_annotation_unlisted_CpGs.R
R/get_annotations.R
R/get_consensusPdb_OverRepresentation.R
R/get_descriptives_GenePosition.R
R/get_descriptives_RelativetoIsland.R
R/get_descriptives_postGWAMA.R
R/get_lambda.R
R/get_low_presence_CpGs.R
R/geteQTMEnrichment.R
R/missMethyl_enrichment.R
R/plot_ChromStates.R
R/plot_Depletion_Enrichment.R
R/plot_GenePosition.R
R/plot_OR.R
R/plot_ProportionHyperGeometrics.R
R/plot_ProportionStatesFP.R
R/plot_RelativetoIsland.R
R/plot_Summary.R
R/plot_TestEnrichDepleit_Collapsed.R
R/plot_TestResults_Collapsed.R
R/plot_TestResults_Collapsed_Positions.R
R/plot_betas_boxplot.R
R/plot_chromosomestate.R
R/plot_distribution.R
R/plot_forestplot.R
R/plot_missMethyl_Summary.R
R/plot_precisionp.R
R/plot_precissionp.R
R/plot_venndiagram.R
R/plot_volcano.R
R/printTableEnrich.R
R/remove_duplicate_CpGs.R
R/restrictCpGstoArtype.R
R/run_GWAMA_MetaAnalysis.R
R/simplifyDuplicates.R
R/summary_HyperGeometrics_Table.R
R/summary_States_FP_Table.R
R/test_duplicate_CpGs.R
R/write_QCData.R
README.md
data/EWASCatalog.RData
data/FP_15_E091.RData
data/FP_18_E091.RData
data/IR_Placenta.RData
data/PMD_placenta.RData
data/crom15.RData
data/dhs.RData
data/eQTM_autosome_unadj_filtered.cells.RData
data/filter_450K.RData
data/filter_EPIC.RData
data/human_c2_v7p1.RData
doc/EASIER.R
doc/EASIER.Rmd
installer.R
man/Chromatin_enrichment.Rd
man/FP_15_E091.Rd
man/FP_18_E091.Rd
man/Hs.c2.Rd
man/IR_Placenta.Rd
man/MSigDB_enrichment.Rd
man/PMD_placenta.Rd
man/addCrom15Columns.Rd
man/addDhsColumns.Rd
man/addGroupColumns.Rd
man/addPhantomSummary.Rd
man/adjust_data.Rd
man/clean_NA_from_data.Rd
man/create_GWAMA_files.Rd
man/crom15.Rd
man/descriptives_CpGs.Rd
man/dhs.Rd
man/eQTM.Rd
man/exclude_CpGs.Rd
man/filterCpGs.Rd
man/filterLowRepresentedCpGsinCohort.Rd
man/filter_450K.Rd
man/filter_EPIC.Rd
man/findOverlapValues.Rd
man/generate_hapmap_file.Rd
man/getAllChromStateOR.Rd
man/getAllChromStateRegressions.Rd
man/getAllFisherTest.Rd
man/getAllHypergeometricTest.Rd
man/getAllRelativeIslandOR.Rd
man/getBinaryClassificationYesNo.Rd
man/getChromStateOR.Rd
man/getChromStateRegression.Rd
man/getEnrichGenomicRanges.Rd
man/getEntrezIdfromSymbol.Rd
man/getFisherTest.Rd
man/getHyperHypo.Rd
man/getHypergeometricTest.Rd
man/getPMDGenomicRanges.Rd
man/getRelativeIslanOR.Rd
man/getUniqueGenes.Rd
man/getUniqueValues.Rd
man/get_annotation_unlisted_CpGs.Rd
man/get_annotattions.Rd
man/get_consensusPdb_OverRepresentation.Rd
man/get_descriptives_GenePosition.Rd
man/get_descriptives_RelativetoIsland.Rd
man/get_descriptives_postGWAMA.Rd
man/get_lambda.Rd
man/get_low_presence_CpGs.Rd
man/geteQTMEnrichment.Rd
man/missMethyl_enrichment.Rd
man/plot_ChromStates.Rd
man/plot_Depletion_Enrichment.Rd
man/plot_ForestPlot.Rd
man/plot_GenePosition.Rd
man/plot_OR.Rd
man/plot_ProportionHyperGeometrics.Rd
man/plot_ProportionStatesFP.Rd
man/plot_RelativetoIsland.Rd
man/plot_Summary.Rd
man/plot_TestEnrichDepleit_Collapsed.Rd
man/plot_TestResults_Collapsed.Rd
man/plot_TestResults_Collapsed_Positions.Rd
man/plot_betas_boxplot.Rd
man/plot_chromosomestate.Rd
man/plot_distribution.Rd
man/plot_missMethyl_Summary.Rd
man/plot_precisionp.Rd
man/plot_precissionp.Rd
man/plot_venndiagram.Rd
man/plot_volcano.Rd
man/printTableEnrich.Rd
man/remove_duplicate_CpGs.Rd
man/restrict_CpGs_to_artype.Rd
man/run_GWAMA_MetaAnalysis.Rd
man/simplifyDuplicates.Rd
man/summary_HyperGeometrics_Table.Rd
man/summary_States_FP_Table.Rd
man/test_duplicate_CpGs.Rd
man/write_QCData.Rd
module_scripts/Enrichment.R
module_scripts/Enrichment_eQTM.R
module_scripts/MetaAnalysis.R
module_scripts/QualityControl.R
news.txt
vignettes/EASIER.Rmd
vignettes/EASIER.Rmd.BACKUP.Rmd
vignettes/EASIER.html
vignettes/EASIER.pdf
vignettes/GWAMA_Results/MetaA1/MetaA1_Fixed_Modif.out
vignettes/bibliography.bib
vignettes/data/Cohort1_Model1_20170713.txt
vignettes/data/Cohort1_Model2_20170713.txt
vignettes/data/PROJ1_Cohort2_Plate_ModelA1_20170309.txt
vignettes/data/PROJ1_Cohort2_Plate_ModelA2_20170309.txt
vignettes/data/PROJ1_Cohort3_Model1_date_v2.txt
vignettes/data/PROJ1_Cohort3_Model2_date_v2.txt
vignettes/imgs/FP_cg22718050.png
vignettes/imgs/Heteroi2.png
vignettes/imgs/Manhat.png
vignettes/imgs/MetaA1_Random.QQ.png
vignettes/imgs/QC/BETAS_BoxPlot.png
vignettes/imgs/QC/precision_SE_N.png
vignettes/imgs/enrich/Enrichment.png
vignettes/imgs/enrich/blood.png
vignettes/imgs/enrich/chr15pla.png
vignettes/imgs/enrich/common.png
vignettes/imgs/enrich/iregions.png
vignettes/imgs/enrich/placenta.png
vignettes/imgs/enrich/plot_genepos.png
vignettes/imgs/enrich/plot_relatisland.png
vignettes/imgs/enrich/pmd_pla.png
vignettes/imgs/meta/manhattan.png
vignettes/imgs/meta/venn.png
vignettes/imgs/precision_SE_N.png
vignettes/imgs/workflows/EnrichmentWorkflow.png
vignettes/imgs/workflows/MetaAnalysisWorkflow.png
vignettes/imgs/workflows/QCWorkflow.png
vignettes/toenrich/CpGstoEnrich.txt
