# Robust outlier identification for DNA methylation data

## Documentation for package ‘epimutacions’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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