GRset                   GRset
UCSC_annotation         UCSC gene annotations
UCSC_regulation         UCSC annotation
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
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
epimutations            Epimutations analysis based on outlier
                        detection methods
epimutations_one_leave_out
                        Epimutations analysis based on outlier
                        detection methods
getBetaParams           Model methylation as a beta distribution
get_ENSEMBL_data        Get ENSEMBL regulatory features overlapping a
                        genomic region
get_candRegsGR          Candidate regions to be epimutations
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
