R/initializeResults.R

In regsplice: L1-regularization based methods for detection of differential splicing

#' @include class_RegspliceData.R class_RegspliceResults.R
NULL




#' Initialize RegspliceResults object.
#' 
#' Initialize a \code{RegspliceResults} object, which will contain the results of the 
#' \code{regsplice} analysis.
#' 
#' Creates a \code{\linkS4class{RegspliceResults}} object containing gene names only. 
#' This object will subsequently be populated using the functions 
#' \code{\link{fitRegMultiple}}, \code{\link{fitNullMultiple}}, 
#' \code{\link{fitFullMultiple}}, and \code{\link{LRTests}}.
#' 
#' Previous step: Calculate \code{limma-voom} transformation and weights with 
#' \code{\link{runVoom}}.
#' Next step: Fit models with \code{\link{fitRegMultiple}}, 
#' \code{\link{fitNullMultiple}}, and \code{\link{fitFullMultiple}}.
#' 
#' 
#' @param rs_data \code{\linkS4class{RegspliceData}} object. This should contain gene IDs
#'   in a column named \code{gene_IDs} in the row meta-data, which can be accessed with 
#'   the accessor function \code{\link{rowData}}.
#' 
#' 
#' @return Returns a \code{\linkS4class{RegspliceResults}} object containing gene IDs 
#'   only.
#' 
#' @seealso \code{\linkS4class{RegspliceData}} \code{\linkS4class{RegspliceResults}} 
#'   \code{\link{fitRegMultiple}} \code{\link{fitNullMultiple}} 
#'   \code{\link{fitFullMultiple}} \code{\link{LRTests}} \code{\link{summaryTable}}
#' 
#' @export
#' 
#' @examples
#' file_counts <- system.file("extdata/vignette_counts.txt", package = "regsplice")
#' data <- read.table(file_counts, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
#' head(data)
#' 
#' counts <- data[, 2:7]
#' tbl_exons <- table(sapply(strsplit(data$exon, ":"), function(s) s[[1]]))
#' gene_IDs <- names(tbl_exons)
#' n_exons <- unname(tbl_exons)
#' condition <- rep(c("untreated", "treated"), each = 3)
#' 
#' rs_data <- RegspliceData(counts, gene_IDs, n_exons, condition)
#' 
#' rs_data <- filterZeros(rs_data)
#' rs_data <- filterLowCounts(rs_data)
#' rs_data <- runNormalization(rs_data)
#' rs_data <- runVoom(rs_data)
#' 
#' rs_results <- initializeResults(rs_data)
#' 
initializeResults <- function(rs_data) {
  
  # unique gene IDs in alphabetical order
  gene_IDs <- names(table(rowData(rs_data)$gene_IDs))
  
  RegspliceResults(gene_IDs)
  
}