Man pages for isglobal-brge/EASIER
EwAS: quality control, meta-analysIs and EnRichment
| addCrom15Columns | Add Chromatine states information |
| addDhsColumns | Add dhs information |
| addGroupColumns | Add group columns from annotation data |
| addPhantomSummary | Add phantom summary |
| adjust_data | Adjust p-value by Bonferroni or FDR |
| Chromatin_enrichment | Get enrichment with Chromatin State and classify hypo i... |
| clean_NA_from_data | Remove NA from data |
| create_GWAMA_files | Creates GWAMA formatted files |
| crom15 | Chromatine states data |
| descriptives_CpGs | CpGs descriptive data |
| dhs | dhs data |
| eQTM | eQTM filter |
| exclude_CpGs | Exclude CpGs |
| filter_450K | 450K Illumina filters |
| filterCpGs | Filter all CpGs |
| filter_EPIC | EPIC Illumina filters |
| filterLowRepresentedCpGsinCohort | Call Rate filter |
| findOverlapValues | Find Overlaps between two genomics ranges |
| FP_15_E091 | Fetal Placenta 15 Stats |
| FP_18_E091 | Fetal Placenta 18 Stats |
| generate_hapmap_file | Create hapmap file for GWAMA |
| getAllChromStateOR | Significative variable OR for all cromatin state |
| getAllChromStateRegressions | Significative variable Regression for all cromatin state |
| getAllFisherTest | Fisher test |
| getAllHypergeometricTest | HyperGeometric Test for positions relative to Island |
| getAllRelativeIslandOR | Significative variable Regression for all relative positions... |
| get_annotation_unlisted_CpGs | Get annotation from unlisted CpGs |
| get_annotattions | Annotate a List of CpGs with Illumina 450K or EPIC data |
| getBinaryClassificationYesNo | Get Binary classification (yes / no) |
| getChromStateOR | Significative variable Regression by cromatin state |
| getChromStateRegression | Significative variable Regression by cromatin state |
| get_consensusPdb_OverRepresentation | Get ConsensusPath Over Representation Enrichment |
| get_descriptives_ChromatineStates | Get descriptives Chromatine States |
| get_descriptives_GenePosition | Get descriptives gene position |
| get_descriptives_ImprintingCarreras | Get descriptives Carreras-Gallo IRC |
| get_descriptives_postGWAMA | Get descriptives after GWAMA |
| get_descriptives_RelativetoIsland | Get descriptives relatives to Island |
| getEnrichGenomicRanges | Create GRanges from data |
| getEntrezIdfromSymbol | Get Entrez gene ID |
| geteQTMEnrichment | Get eQTM enrichment |
| getFisherTest | Get Fisher test for significative variable attending to... |
| getHypergeometricTest | HyperGeometric Test for positions relative to Island |
| getHyperHypo | Get Hiper and Hipo methylation data |
| get_lambda | Get lambda |
| get_low_presence_CpGs | Get CpGs with low presence |
| getPMDGenomicRanges | Create GRanges from PMD |
| getRelativeIslanOR | Significative variable OR by position Relative to Island |
| getUniqueGenes | Get unique genes |
| getUniqueValues | Get unique values in vector |
| Hs.c2 | Molecular Signatures Database (MSigDB v 7.1) - C2 curated... |
| IRCarreras_Ev1 | Imprinting Regions Carreras-Gallo Epic V1 |
| IRCarreras_Ev2 | Imprinting Regions Carreras-Gallo Epic V2 |
| IR_Placenta | Imprinting Regions Placenta |
| missMethyl_enrichment | Get Pathways enrichment with missMethyl |
| MSigDB_enrichment | Get enrichment with Molecular Signatures Database (MSigDB) |
| plot_betas_boxplot | Betas Boxplot |
| plot_chromosomestate | Chromosome State Plot |
| plot_ChromStates | Plot ChromStates |
| plot_Depletion_Enrichment | Depletion and Enrichment Plot |
| plot_distribution | Distribution plot |
| plot_ForestPlot | Forest plot |
| plot_GenePosition | Gene Pisition Plots |
| plot_missMethyl_Summary | Plot enrichment summary |
| plot_OR | Plot OR |
| plot_precisionp | Precision plot |
| plot_precissionp | Precission plot |
| plot_ProportionHyperGeometrics | Chromosome State Plot |
| plot_ProportionStatesFP | Chromosome State Plot |
| plot_RelativetoIsland | Relative to Island Plot |
| plot_Summary | Plot enrichment summary |
| plot_TestEnrichDepleit_Collapsed | Plot collapsed tests results |
| plot_TestResults_Collapsed | Plot collapsed tests results |
| plot_TestResults_Collapsed_Positions | Plot collapsed tests results for positions |
| plot_venndiagram | Venn diagrams plots |
| plot_volcano | Volcano plot |
| PMD_placenta | PMD placenta |
| printTableEnrich | Print table with enrichment data |
| remove_duplicate_CpGs | Remove duplicate CpGs |
| restrict_CpGs_to_artype | Restrict CpGs to array type |
| run_GWAMA_MetaAnalysis | Run GWAMA meta-analysis |
| simplifyDuplicates | Get unique values in a cell |
| summary_HyperGeometrics_Table | Summarized States Fetal Placenta for significant, hyper and... |
| summary_States_FP_Table | Summarized States Fetal Placenta for significant, hyper and... |
| test_duplicate_CpGs | Test duplicate CpGs |
| write_QCData | Write QC results to a file |
