Package: epimutacions 1.11.0

Dolors Pelegri-Siso

epimutacions: Robust outlier identification for DNA methylation data

The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.

Authors:Dolors Pelegri-Siso [aut, cre], Juan R. Gonzalez [aut], Carlos Ruiz-Arenas [aut], Carles Hernandez-Ferrer [aut], Leire Abarrategui [aut]

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epimutacions.pdf |epimutacions.html✨
epimutacions/json (API)
NEWS

# Install 'epimutacions' in R:
install.packages('epimutacions', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/isglobal-brge/epimutacions/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:epimutacions-1.11.0(bioc 3.21)epimutacions-1.10.0(bioc 3.20)

dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp

4.23 score 28 scripts 190 downloads 7 exports 214 dependencies

Last updated 4 months agofrom:8a6e409213. Checks:1 ERROR, 8 WARNING, 2 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesFAILFeb 17 2025
R-4.5-win-x86_64WARNINGFeb 17 2025
R-4.5-mac-x86_64WARNINGFeb 17 2025
R-4.5-mac-aarch64WARNINGFeb 17 2025
R-4.5-linux-x86_64WARNINGFeb 17 2025
R-4.4-win-x86_64WARNINGFeb 17 2025
R-4.4-mac-x86_64WARNINGFeb 17 2025
R-4.4-mac-aarch64WARNINGFeb 17 2025
R-4.3-win-x86_64WARNINGFeb 17 2025
R-4.3-mac-x86_64NOTEDec 19 2024
R-4.3-mac-aarch64NOTEDec 19 2024

Exports:annotate_epimutationsepi_parametersepi_preprocessepimutationsepimutations_one_leave_outnorm_parametersplot_epimutations

Dependencies:abindannotateAnnotationDbiAnnotationFilterAnnotationHubaskpassbackportsbase64base64encbeanplotBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibbumphuntercachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirDEoptimRdichromatdigestdoRNGdplyrensembldbepimutacionsDataevaluateExperimentHubfansifarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2ggrepelglueGO.dbgraphgridExtragtableGvizh5mreadHDF5ArrayhighrHmischmsHomo.sapienshtmlTablehtmltoolshtmlwidgetshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b2.hg19IlluminaHumanMethylationEPICmanifestilluminaiointerpIRangesisobandisotreeiteratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimeminfimulttestmunsellnlmennetnor1mixopensslorg.Hs.eg.dbOrganismDbipillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogressProtGenericspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRcppEigenRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhpcBLASctlRhtslibrjsonrlangrmarkdownrngtoolsrobustbaserpartRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4VectorssassscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg18.knownGeneTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGenetxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Add ENSEMBL regulatory regions to epimutationsadd_ensemble_regulatory
Annotate the DMR resulting from epimutacions packageannotate_cpg
Annotate the results of epimutations or epimutations_one_leave_out functionsannotate_epimutations
Obtains bumps beta valuesbetas_from_bump
Computes beta values, standard deviation and mean to plot the epimutationbetas_sd_mean
Sets common column names in a data framecols_names
Generates a GRanges objectcreate_GRanges_class
Identifies epimutations based on a beta distribution.epi_beta
Identifies epimutations using Isolation Forestepi_iForest
Identifies epimutations using Robust Mahalanobis distanceepi_mahdist
Identifies epimutations using MANOVAepi_manova
Detects epimutations using Multivariate Linear Model (MLM)epi_mlm
Settings for parameters of 'epimutations' and 'epimutations_one_leave_out' functionsepi_parameters
Preprocess methylation arrayepi_preprocess
Identifies epimutations using quantile distributionepi_quantile
Epimutations analysis based on outlier detection methodsepimutations
Epimutations analysis based on outlier detection methodsepimutations_one_leave_out
Candidate regions to be epimutationsget_candRegsGR
Get ENSEMBL regulatory features overlapping a genomic regionget_ENSEMBL_data
Model methylation as a beta distributiongetBetaParams
GRsetGRset
Merge records for the same ENSEMBL regulatory elementmerge_records
Non-parametric, Asymptotic P-values for Multivariate Linear Modelsmlm
Settings for parameters of epi_preprocess functionnorm_parameters
Plot a given epimutation and locate it along the genomeplot_epimutations
Process data from ENSEMBLprocess_ENSEMBL_results
Creates a data frame containing the results obtained from Isolation Forestres_iForest
Creates a data frame containing the results obtained from Robust Mahalanobis distanceres_mahdist
Creates a data frame containing the results obtained from MANOVAres_manova
Creates a data frame containing the results obtained from MLMres_mlm
res.epi.manovares.epi.manova
UCSC gene annotationsUCSC_annotation
UCSC annotationUCSC_regulation