R/check_se_rownames.R

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

check_se_rownames <- function(obj,
                              rownames_var=NULL,
                              remove_duplicates=TRUE,
                              verbose=TRUE){

  messager("+ Checking obj rownames.",v=verbose)
  rowDat <- SummarizedExperiment::rowData(obj)
  rownames_var <- if(is.null(rownames_var)) "Gene" else rownames_var
  if(is.null( S4Vectors::rownames(rowDat)) ){
    if(rownames_var %in% colnames(rowDat)){
      messager("+ Assigning rownames to:",rownames_var,v=verbose)
      # IMPORTANT! only S4Vectors::rownames can assign row names.
      # Automatically assigns same rownames to assay and rowData
      S4Vectors::rownames(obj) <- rowDat[[rownames_var]]

    } else {
      S4Vectors::rownames(obj) <- rownames(obj@assays@data[[1]])
    }
  }
  if(isTRUE(remove_duplicates)){
    dup_rows <- base::duplicated(S4Vectors::rownames(obj))
    if(sum(dup_rows)>0){
      messager("+ Removing duplicate gene rows.",v=verbose)
      obj <- obj[!dup_rows,]
    }
  }
  return(obj)
}