Robust outlier identification for DNA methylation data

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Documentation for package ‘epimutacions’ version 1.11.0

• 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