R/DEFormats.R

In DEFormats: Differential gene expression data formats converter

#' Convert Between Differential Gene Expression Data Formats
#' 
#' \pkg{DEFormats} provides data converters between various formats used by 
#' different gene expression analysis packages.
#' 
#' Currently the package supports data conversion between \pkg{DESeq2} and 
#' \pkg{edgeR}, i.e., between \code{\linkS4class{DESeqDataSet}} and 
#' \code{\linkS4class{DGEList}} objects, respectively.
#' 
#' Objects can be coerced using the following methods \itemize{ \item 
#' \code{\link{as.DESeqDataSet}} \item \code{\link{as.DGEList}} }
#' @template author
#' @docType package
#' @name DEFormats
#' @import data.table
#' @importFrom checkmate qassert
#' @importFrom edgeR DGEList
#' @importClassesFrom edgeR DGEList
#' @importFrom DESeq2 DESeqDataSetFromMatrix normalizationFactors counts design 
#'   normalizationFactors<- makeExampleDESeqDataSet
#' @importClassesFrom DESeq2 DESeqDataSet
#' @importFrom SummarizedExperiment rowData rowRanges colData assay
#'   as.data.frame SummarizedExperiment mcols<-
#' @importFrom GenomicRanges GRanges makeGRangesListFromDataFrame
#' @importClassesFrom GenomicRanges GenomicRanges_OR_GRangesList
#' @importFrom methods as is new setAs setGeneric setMethod
#' @importFrom stats formula runif terms
#' @importFrom S4Vectors DataFrame
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