R/ascend_getters.R

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

################################################################################
#
# ascend_getters.R
# description: Methods related to the retrieval of data into an EMSet.
#
################################################################################

#' regcounts
#' 
#' Convenience method to access regressed counts from an \linkS4class{EMSet}.
#' 
#' @param x \linkS4class{EMSet} 
#' @param ... ...
#' 
#' @examples
#' # Load em_set
#' em_set <- ascend::analyzed_set
#' 
#' # Regress out CDK4
#' reg_set <- regressConfoundingFactors(em_set, candidate.genes = "CDK4")
#' 
#' # Access regressed matrix
#' reg_counts <- regcounts(reg_set)
#' 
#' @return Regressed count matrix
#' @include ascend_objects.R
#' @include ascend_confoundingfactors.R
#' @export
setGeneric("regcounts", function(x, ...) 
  standardGeneric("regcounts"))

#' @rdname regcounts
setMethod("regcounts", "EMSet", function(x){
  if ("regcounts" %in% SummarizedExperiment::assayNames(x)){
    assays <- SummarizedExperiment::assays(x)
    counts <- assays$regcounts
    return(counts)
  }
})

#' clusterAnalysis
#' 
#' Convenience method to access cluster analysis data from an 
#' \linkS4class{EMSet}.
#' 
#' @param x \linkS4class{EMSet} 
#' @param ... ...
#' 
#' @examples
#' 
#' # Load analysed EMSet
#' em_set <- ascend::analyzed_set
#' 
#' cluster_analysis <- clusterAnalysis(em_set)
#' 
#' @return List of cluster-related analyses
#' @include ascend_objects.R
#' @export
setGeneric("clusterAnalysis", function(x, ...) 
  standardGeneric("clusterAnalysis"))

#' @rdname clusterAnalysis
setMethod("clusterAnalysis", "EMSet", function(x){
  output <- x@clusterAnalysis
  return(output)
})

#' controls
#' 
#' Access set controls.
#' 
#' @param x \linkS4class{EMSet}
#' @param ... ...
#' 
#' @examples
#' # Load EMSet
#' em_set <- ascend::raw_set
#' 
#' # Access controls
#' controls <- controls(em_set)
#' 
#' # Set controls
#' controls(em_set) <- controls
#' 
#' @include ascend_objects.R
#' @export
setGeneric("controls", function(x, ...) standardGeneric("controls"))

#' @rdname controls
setMethod("controls", "EMSet", function(x){
  controls <- x@log$set_controls
  return(controls)
})

#' progressLog
#' 
#' Access log stored in the \linkS4class{EMSet}.
#' 
#' @param x \linkS4class{EMSet}
#' @param ... ...
#' @return A list of information.
#' 
#' @examples
#' # Load EMSet
#' em_set <- ascend::analyzed_set
#' 
#' # Retrieve progress log
#' log <- progressLog(em_set)
#' 
#' # Set progressLog
#' progressLog(em_set) <- log
#' 
#' @include ascend_objects.R
#' @export
setGeneric("progressLog", function(x, ...) standardGeneric("progressLog"))

#' @rdname progressLog
setMethod("progressLog", signature(x = "EMSet"), function(x){
  output <- x@log
  return(output)
})

#' colInfo
#' 
#' Access cell information stored in colInfo.
#' 
#' @param x \linkS4class{EMSet}
#' @param ... ...
#' @param withDimnames Retrieve rownames of DataFrame Default: TRUE
#' 
#' @return colInfo DataFrame
#' 
#' @examples 
#' # Load EMSet
#' em_set <- ascend::raw_set
#' 
#' # Retrieve colInfo
#' column_info <- colInfo(em_set)
#' 
#' # Set colInfo
#' colInfo(em_set) <- column_info
#' 
#' @include ascend_objects.R
#' @importFrom BiocGenerics rownames
#' @export
setGeneric("colInfo", function(x, ...) standardGeneric("colInfo"))

#' @rdname colInfo
setMethod("colInfo", "EMSet", function(x, withDimnames = TRUE){
  output <- x@colInfo
  
  # If user has set withDimnames
  if (withDimnames){
    BiocGenerics::rownames(output) <- colnames(x)
  }
  return(output)
})
 
#' rowInfo
#' 
#' Access gene information stored in rowInfo.
#'
#' @param x \linkS4class{EMSet}
#' @param ... ...
#' @param withDimnames TRUE or FALSE
#' 
#' @return rowInfo DataFrame
#' 
#' @examples
#' 
#' # Load EMSet
#' em_set <- ascend::raw_set
#' 
#' # Retrieve colInfo
#' row_info <- rowInfo(em_set)
#' 
#' # Set colInfo
#' rowInfo(em_set) <- row_info
#' 
#' @include ascend_objects.R
#' @importFrom BiocGenerics rownames
#' @export
setGeneric("rowInfo", function(x, ...) standardGeneric("rowInfo"))

#' @rdname rowInfo
setMethod("rowInfo", "EMSet", function(x, withDimnames = TRUE){
  output <- x@rowInfo
  if (withDimnames){
    BiocGenerics::rownames(output) <- rownames(x)
  }
  return(output)
})
 
#' Subsetter for EMSet
#' 
#' @param x An \linkS4class{EMSet}
#' @param i Row index
#' @param j Col index
#' @param drop Drop stuff
#' 
#' @return Subsetted EMSet
#' 
setMethod("[", "EMSet", function(x, i, j, drop=TRUE) {
  # Extract infos from original dataset
  col_info <- colInfo(x, withDimnames=FALSE)
  row_info <- rowInfo(x, withDimnames=FALSE)
  
  # If row is defined
  if (!missing(i)) {
    if (is.character(i)) {
      fmt <- paste0("<", class(x), ">[i,] index out of bounds: %s")
      i <- SummarizedExperiment:::.SummarizedExperiment.charbound(
        i, rownames(x), fmt
      )
    }
    i <- as.vector(i)
    row_info <- row_info[i, , drop = drop]
  }
  
  # If column is defined
  if (!missing(j)) {
    if (is.character(j)) {
      fmt <- paste0("<", class(x), ">[,j] index out of bounds: %s")
      j <- SummarizedExperiment:::.SummarizedExperiment.charbound(
        j, colnames(x), fmt
      )
    }
    j <- as.vector(j)
    col_info <- col_info[j, ,drop=drop]
  }
  
  out <- callNextMethod()
  out <- BiocGenerics:::replaceSlots(out, colInfo = col_info, rowInfo = row_info, check=FALSE)
  out <- calculateQC(out)
  out
})