R/seurat_to_list.R

In bschilder/scKirby: Automated ingestion and conversion of various single-cell data formats.

#' Convert: \code{Seurat} ==> \code{list}
#'
#' @inheritParams converters
#' @returns A named list.
#'
#' @export
#' @examples
#' obj <- example_obj("seurat")
#' obj2 <- seurat_to_list(obj)
seurat_to_list <- function(obj,
                           verbose=TRUE){

  messager_to()
  if(methods::is(obj,"seurat")){
    seurat1_to_list(obj = obj,
                    verbose = verbose)
  } else {
    messager("+ Seurat ==> list",v=verbose)
    list(
      data = get_x(obj = obj,
                      verbose = verbose),
      obs = get_obs(obj = obj,
                    verbose = verbose),
      var = get_var(obj = obj,
                    verbose = verbose),
      obsm = get_obsm(obj = obj,
                      verbose = verbose),
      varm = get_varm(obj = obj,
                      verbose = verbose),
      graphs = get_obsp(obj = obj,
                          verbose = verbose),
      uns = get_uns(obj = obj,
                    verbose = verbose)
    )
  }

}