Package: epimutacions 1.17.2

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]

# 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:

GRset - GRset
res.epi.manova - Res.epi.manova

On BioConductor:epimutacions-1.17.2(bioc 3.24)epimutacions-1.16.2(bioc 3.23)

dnamethylation biologicalquestion preprocessing statisticalmethod normalization cpp

5.53 score 38 scripts 456 downloads 7 exports 153 dependencies

Last updated from:c1ba7966ba. Checks:1 NOTE, 15 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	421
linux-devel-arm64	OK	726
linux-devel-x86_64	OK	852
source / vignettes	OK	822
linux-release-arm64	OK	684
linux-release-x86_64	OK	868
macos-release-arm64	OK	693
macos-release-x86_64	OK	1152
macos-oldrel-arm64	OK	432
macos-oldrel-x86_64	OK	925
windows-devel-arm64	OK	466
windows-devel-x86_64	OK	711
windows-release-arm64	OK	675
windows-release-x86_64	OK	684
windows-oldrel-x86_64	OK	740
wasm-release	OK	491

Exports:annotate_epimutations epi_parameters epi_preprocess epimutations epimutations_one_leave_out norm_parameters plot_epimutations

Dependencies:abind annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel biomaRt Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats DEoptimR digest dir.expiry doRNG dplyr epimutacionsData farver fastmap filelock foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable h5mread HDF5Array hms httr httr2 illuminaio IRanges isoband isotree iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nor1mix openssl pillar pkgconfig plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl readr rentrez reshape restfulr rhdf5 rhdf5filters Rhdf5lib RhpcBLASctl Rhtslib rjson rlang rngtools robustbase Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml

The epimutacions User's Guide

Rendered fromepimutacions.Rmdusingknitr::rmarkdown

Last update: 2026-09-10
Started: 2021-04-07

Help page	Topics
Add ENSEMBL regulatory regions to epimutations	add_ensemble_regulatory
Annotate the DMR resulting from epimutacions package	annotate_cpg
Annotate the results of epimutations or epimutations_one_leave_out functions	annotate_epimutations
Obtains bumps beta values	betas_from_bump
Computes beta values, standard deviation and mean to plot the epimutation	betas_sd_mean
Sets common column names in a data frame	cols_names
Generates a GRanges object	create_GRanges_class
Identifies epimutations based on a beta distribution.	epi_beta
Identifies epimutations using Isolation Forest	epi_iForest
Identifies epimutations using Robust Mahalanobis distance	epi_mahdist
Identifies epimutations using MANOVA	epi_manova
Detects epimutations using Multivariate Linear Model (MLM)	epi_mlm
Settings for parameters of 'epimutations' and 'epimutations_one_leave_out' functions	epi_parameters
Preprocess methylation array	epi_preprocess
Identifies epimutations using quantile distribution	epi_quantile
Epimutations analysis based on outlier detection methods	epimutations
Epimutations analysis based on outlier detection methods	epimutations_one_leave_out
Candidate regions to be epimutations	get_candRegsGR
Get ENSEMBL regulatory features overlapping a genomic region	get_ENSEMBL_data
Model methylation as a beta distribution	getBetaParams
GRset	GRset
Merge records for the same ENSEMBL regulatory element	merge_records
Non-parametric, Asymptotic P-values for Multivariate Linear Models	mlm
Settings for parameters of epi_preprocess function	norm_parameters
Plot a given epimutation and locate it along the genome	plot_epimutations
Process data from ENSEMBL	process_ENSEMBL_results
Creates a data frame containing the results obtained from Isolation Forest	res_iForest
Creates a data frame containing the results obtained from Robust Mahalanobis distance	res_mahdist
Creates a data frame containing the results obtained from MANOVA	res_manova
Creates a data frame containing the results obtained from MLM	res_mlm
res.epi.manova	res.epi.manova
UCSC gene annotations	UCSC_annotation
UCSC annotation	UCSC_regulation

Package: epimutacions 1.17.2

epimutacions: Robust outlier identification for DNA methylation data

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)