REMP: Repetitive Element Methylation Prediction

#' @title Repetitive Element Methylation Prediction
#'
#' @description
#' Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE)
#' by learning surrounding genetic and epigenetic information. These tools provide genomewide and
#' single-base resolution of DNA methylation prediction on RE that are difficult to measure directly using
#' array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS)
#' and differentially methylated region (DMR) analysis on RE.
#'
#' @name REMP-package
#'
#' @aliases REMP-package REMP
#'
#' @docType package
#'
#' @section Overview - standard procedure:
#' \describe{
#'     \item{Step 1}{Start out generating required dataset for prediction using \code{\link{initREMP}}.
#'     The datasets include RE information, RE-CpG (i.e. CpGs located in RE region) information,
#'     and gene annotation, which are maintained in a \code{\link{REMParcel}} object.
#'     It is recommended to save these generated data to the working directory so they can be used in the future.}
#'     \item{Step 2}{Clean Illumina methylation dataset using \code{\link{grooMethy}}. This function
#'     can help identify and fix abnormal values and automatically impute missing values, which are
#'     essential for downstream prediction.}
#'     \item{Step 3}{Run \code{\link{remp}} to predict genome-wide locus specific RE methylation.}
#'     \item{Step 4}{Use the built-in accessors and utilities in \code{\link{REMProduct}} object to get or
#'     refine the prediction results.}
#'     }
#'
#' @author
#' Yinan Zheng \email{y-zheng@@northwestern.edu},
#' Lei Liu \email{lei.liu@@northwestern.edu},
#' Wei Zhang \email{wei.zhang1@@northwestern.edu},
#' Warren Kibbe \email{warren.kibbe@@nih.gov},
#' Lifang Hou \email{l-hou@@northwestern.edu}
#'
#' Maintainer: Yinan Zheng \email{y-zheng@@northwestern.edu}
#'
#' @references Zheng Y, Joyce BT, Liu L, Zhang Z, Kibbe WA, Zhang W, Hou L.
#' Prediction of genome-wide DNA methylation in repetitive elements.
#' Nucleic Acids Res. 2017;45(15):8697-711.
#' PubMed PMID: 28911103; PMCID: PMC5587781.
#' http://dx.doi.org/10.1093/nar/gkx587.
#'
#' @keywords package
#'
#' @import methods
#' @import S4Vectors
#' @import BiocParallel
#' @import caret
#' @importFrom SummarizedExperiment SummarizedExperiment rowRanges assays rowData colData
#' @importFrom minfi getAnnotation getBeta getM MethylSet RatioSet GenomicRatioSet IlluminaMethylationAnnotation
#' @importFrom readr read_delim cols_only col_character col_integer
#' @importFrom rtracklayer liftOver
#' @importFrom impute impute.knn
#' @importFrom kernlab predict
#' @importFrom ranger ranger importance
#' @importFrom settings stop_if_reserved reset options_manager
#' @importFrom stats setNames density na.pass
#' @importFrom utils download.file read.table data packageVersion
#' @importFrom graphics lines plot
#' @importFrom AnnotationHub AnnotationHub getAnnotationHubOption setAnnotationHubOption
#' @importFrom iterators nextElem idiv
#' @importFrom org.Hs.eg.db org.Hs.egREFSEQ2EG org.Hs.egSYMBOL
#' @importFrom GenomicRanges GRanges GRangesList makeGRangesListFromFeatureFragments findOverlaps
#' @importFrom GenomicRanges granges seqnames start end strand ranges promoters shift start<- end<-
#' @importFrom IRanges IRanges IRangesList CharacterList NumericList subsetByOverlaps
#' @importFrom GenomeInfoDb seqlevels<-
#' @importFrom parallel detectCores
#' @importFrom doParallel registerDoParallel
#' @importFrom foreach registerDoSEQ
#' @importFrom BiocGenerics mget
#' @importFrom BSgenome getSeq
#' @importFrom Biostrings DNAString vmatchPattern
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