R/methods-cell_data_set.R

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

#' Methods for the cell_data_set class
#' @name cell_data_set-methods
#' @docType methods
#' @rdname cell_data_set-methods
#' @param object The cell_data_set object
setValidity( "cell_data_set", function( object ) {
  TRUE
} )

#' Set the size factor values in the cell_data_set
#'
#' @param cds A cell_data_set object.
#' @param value the size factor values.
#' @return An updated cell_data_set object
`size_factors<-` <- function( cds, value ) {
  stopifnot( methods::is( cds, "cell_data_set" ) )
  colData(cds)$Size_Factor <- value
  methods::validObject( cds )
  cds
}

#' Get the size factors from a cds object.
#'
#' A wrapper around \code{colData(cds)$Size_Factor}
#'
#' @param cds A cell_data_set object.
#' @return An updated cell_data_set object
#'
#' @examples
#'   \donttest{
#'     cds <- load_a549()
#'     size_factors(cds)
#'   }
#'
#' @export
size_factors <- function( cds ) {
  stopifnot( methods::is( cds, "cell_data_set" ) )
  sf <- colData(cds)$Size_Factor
  names( sf ) <- colnames( SingleCellExperiment::counts(cds) )
  sf
}