--- a
+++ b/R/metadata.R
@@ -0,0 +1,1107 @@
+#' @importClassesFrom data.table data.table
+
+####
+# Objects and Classes ####
+####
+
+### $ methods ####
+
+#' @method $ vrMetadata
+#'
+"$.vrMetadata" <- function(x, i, ...) {
+  return(NULL)
+}
+
+#' @method $<- vrMetadata
+#'
+#' @importFrom methods new slot
+"$<-.vrMetadata" <- function(x, i, ..., value) {
+
+  # molecule metadata
+  mol.metadata <- methods::slot(x, "molecule")
+  if(nrow(mol.metadata) > 0)
+    mol.metadata[[i]] <- value
+
+  # cell metadata
+  cell.metadata <- methods::slot(x, "cell")
+  if(nrow(cell.metadata) > 0)
+    cell.metadata[[i]] <- value
+
+  # spot metadata
+  spot.metadata <- methods::slot(x, "spot")
+  if(nrow(spot.metadata) > 0)
+    spot.metadata[[i]] <- value
+
+  # ROI metadata
+  roi.metadata <- methods::slot(x, "ROI")
+  if(nrow(roi.metadata) > 0)
+    roi.metadata[[i]] <- value
+
+  # ROI metadata
+  tile.metadata <- methods::slot(x, "tile")
+  if(nrow(tile.metadata) > 0)
+    tile.metadata[[i]] <- value
+
+  return(methods::new("vrMetadata", molecule = mol.metadata, cell = cell.metadata, spot = spot.metadata, ROI = roi.metadata, tile = tile.metadata))
+}
+
+#' @method $<- vrMetadata
+#'
+#' @importFrom methods new slot
+#'
+"[[<-.vrMetadata" <- function(x, i, ..., value) {
+
+  # molecule metadata
+  mol.metadata <- methods::slot(x, "molecule")
+  if(nrow(mol.metadata) > 0)
+    mol.metadata[[i]] <- value
+
+  # cell metadata
+  cell.metadata <- methods::slot(x, "cell")
+  if(nrow(cell.metadata) > 0)
+    cell.metadata[[i]] <- value
+
+  # spot metadata
+  spot.metadata <- methods::slot(x, "spot")
+  if(nrow(spot.metadata) > 0)
+    spot.metadata[[i]] <- value
+
+  # ROI metadata
+  roi.metadata <- methods::slot(x, "ROI")
+  if(nrow(roi.metadata) > 0)
+    roi.metadata[[i]] <- value
+
+  # ROI metadata
+  tile.metadata <- methods::slot(x, "tile")
+  if(nrow(tile.metadata) > 0)
+    tile.metadata[[i]] <- value
+
+  return(methods::new("vrMetadata", molecule = mol.metadata, cell = cell.metadata, spot = spot.metadata, ROI = roi.metadata, tile = tile.metadata))
+}
+
+####
+# Methods ####
+####
+
+vrSpatialPointsvrMetadata <- function(object, assay = NULL) {
+  
+  # get spatial points
+  points <- unlist(lapply(methods::slotNames(object), function(x) {
+    if(x %in% c("cell", "spot", "ROI")){
+      mdata <- slot(object, name = x)
+      if(nrow(mdata) > 0){
+        if(!is.null(rownames(mdata))){
+          sp <- rownames(mdata)
+        } else {
+          sp <- as.vector(mdata$id)
+        }
+        if(!is.null(assay))
+          sp <- sp[grepl(paste(paste0(assay, "$"), collapse = "|"), sp)]
+        return(sp)  
+      }
+    } else {
+      mdata <- slot(object, name = x)
+      if(nrow(mdata) > 0){
+        if(inherits(mdata, "data.table")){
+          if(!is.null(assay))
+            sp <- subset(mdata, subset = assay_id %in% assay)
+          return(sp[["id"]])
+        } else {
+          sp <- as.vector(mdata$id)
+          if(!is.null(assay))
+            sp <- sp[grepl(paste(paste0(assay, "$"), collapse = "|"), sp)]
+          return(sp)
+        }
+      }
+    }
+  }))
+  
+  # return points
+  return(points)
+}
+
+#' @param assay assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 
+#' if NULL, the default assay will be used, see \link{vrMainAssay}.
+#'
+#' @rdname vrSpatialPoints
+#' @order 3
+#'
+#' @importFrom methods slotNames
+#'
+#' @export
+setMethod("vrSpatialPoints", "vrMetadata", vrSpatialPointsvrMetadata)
+
+subsetvrMetadata <- function(x, subset, samples = NULL, assays = NULL, spatialpoints = NULL) {
+  
+  # start 
+  object <- x
+  
+  if (!missing(x = subset)) {
+    subset <- enquo(arg = subset)
+  }
+  
+  # subset all metadata types
+  if(!is.null(samples)){
+    if(nrow(object@molecule) > 0){
+      mol.metadata <- subset_metadata(object@molecule, samples = samples)
+    } else {
+      mol.metadata <- data.table::data.table()
+    }
+    cell.metadata <- subset_metadata(object@cell, samples = samples)
+    spot.metadata <- subset_metadata(object@spot, samples = samples)
+    roi.metadata <- subset_metadata(object@ROI, samples = samples)
+    if(nrow(object@tile) > 0){
+      tile.metadata <- subset_metadata(object@tile, samples = samples)
+    } else {
+      tile.metadata <- data.table::data.table()
+    }
+  } else if(!is.null(assays)){
+    assay_names <- unique(lapply(slotToList(object), function(x) {
+      if(inherits(x, "data.table")){
+        return(unique(as.vector(x$assay_id)))
+      } else {
+        if(!is.null(rownames(x))){
+          return(unique(stringr::str_extract(rownames(x), "Assay[0-9]+")))
+        } else {
+          return(unique(stringr::str_extract(as.vector(x$id), "Assay[0-9]+"))) 
+        }
+      }
+    }))
+    assay_names <- unique(do.call(c,assay_names))
+    if(all(assays %in% assay_names)){
+      if(nrow(object@molecule) > 0) {
+        mol.metadata <- subset_metadata(object@molecule, assays = assays)
+      } else {
+        mol.metadata <- data.table::data.table()
+      }
+      cell.metadata <- subset_metadata(object@cell, assays = assays)
+      spot.metadata <- subset_metadata(object@spot, assays = assays)
+      roi.metadata <- subset_metadata(object@ROI, assays = assays)
+      if(nrow(object@tile) > 0) {
+        tile.metadata <- object@tile[assay_id %in% assays, ]
+      } else {
+        tile.metadata <- data.table::data.table()
+      }
+    } else {
+      if(nrow(object@molecule) > 0) {
+        mol.metadata <- subset_metadata(object@molecule, assaytypes = assays)
+      } else {
+        mol.metadata <- data.table::data.table()
+      }
+      cell.metadata <- subset_metadata(object@cell, assaytypes = assays)
+      spot.metadata <- subset_metadata(object@spot, assaytypes = assays)
+      roi.metadata <- subset_metadata(object@ROI, assaytypes = assays)
+      if(nrow(object@tile) > 0) {
+        tile.metadata <- subset_metadata(object@tile, assaytypes = assays)
+      } else {
+        tile.metadata <- data.table::data.table()
+      }
+    }
+  } else if(!is.null(spatialpoints)){
+    if(nrow(object@molecule) > 0){
+      mol.metadata <- subset_metadata(object@molecule, spatialpoints = spatialpoints)
+    } else {
+      mol.metadata <- data.table::data.table()
+    }
+    cell.metadata <- subset_metadata(object@cell, spatialpoints = spatialpoints)
+    spot.metadata <- subset_metadata(object@spot, spatialpoints = spatialpoints)
+    roi.metadata <- subset_metadata(object@ROI, spatialpoints = spatialpoints)
+    if(nrow(object@tile) > 0){
+      tile.metadata <- subset_metadata(object@tile, spatialpoints = spatialpoints)
+    } else {
+      tile.metadata <- data.table::data.table()
+    }
+  } else {
+    stop("No assay, sample or spatial points were provided!")
+  }
+  
+  # return new metadata
+  methods::new("vrMetadata",
+               molecule = mol.metadata,
+               cell = cell.metadata,
+               spot = spot.metadata,
+               ROI = roi.metadata,
+               tile = tile.metadata)
+}
+
+#' Subsetting vrMetadata objects
+#'
+#' Given a vrMetadata object, subset the object given one of the attributes
+#'
+#' @param x a vrMetadata object
+#' @param subset the subset statement
+#' @param samples the set of samples to subset the object
+#' @param assays assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \code{SampleMetadata(object)}
+#' @param spatialpoints the set of spatial points to subset the object
+#'
+#' @method subset vrMetadata
+#' @order 3
+#'
+#' @importFrom rlang enquo
+#' @importFrom stringr str_extract
+#' @importFrom data.table setkey
+setMethod("subset", "vrMetadata", subsetvrMetadata)
+
+#' subset_sampleMetadata
+#'
+#' Subseting sample metadata
+#'
+#' @param metadata sample metadata of a VoltRon object
+#' @param samples the set of samples to subset the object
+#' @param assay assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 
+#' if NULL, the default assay will be used, see \link{vrMainAssay}.
+#'
+#' @noRd
+subset_sampleMetadata <- function(metadata, samples = NULL, assays = NULL) {
+
+  # subseting on samples, layers and assays
+  if(!is.null(samples)){
+    if(all(samples %in% metadata$Sample)){
+      metadata <- metadata[metadata$Sample %in% samples,]
+    } else {
+      stop("Some samples with the names '", paste(samples, collapse = ", "), "' are not found in the object")
+    }
+  } else if(!is.null(assays)) {
+    if(all(assays %in% rownames(metadata))){
+      metadata <- metadata[assays,]
+    } else if(all(assays %in% metadata$Assay)){
+      metadata <- metadata[metadata$Assay %in% assays,]
+    } else {
+      stop("Some assay with the names or types '", paste(assays, collapse = ", "), "' are not found in the object")
+    }
+  }
+  metadata
+}
+
+mergevrMetadata <- function(x, y) {
+
+  # start 
+  object <- x
+  object_list <- y
+  
+  # combine all elements
+  if(!is.list(object_list))
+    object_list <- list(object_list)
+  object_list <- c(object, object_list)
+
+  # check if all are VoltRon
+  if(!all(lapply(object_list, class) == "vrMetadata"))
+    stop("All arguements have to be of vrMetadata class")
+
+  # choose objects
+  obj1 <- object_list[[1]]
+  obj2 <- object_list[[2]]
+
+  # initial combination
+  if(length(object_list) > 2){
+    combined.metadata <- mergevrMetadata(obj1, obj2)
+    for(i in 3:(length(object_list))){
+      combined.metadata <- mergevrMetadata(combined.metadata, object_list[[i]])
+    }
+  } else {
+    updateobjects <- updateMetadataAssay(obj1, obj2)
+    obj1 <- updateobjects$object1
+    obj2 <- updateobjects$object2
+    mol.metadata <- rbind_metadata(methods::slot(obj1, "molecule"), methods::slot(obj2, "molecule"))
+    cell.metadata <- rbind_metadata(methods::slot(obj1, "cell"), methods::slot(obj2, "cell"))
+    spot.metadata <- rbind_metadata(methods::slot(obj1, "spot"), methods::slot(obj2, "spot"))
+    roi.metadata <- rbind_metadata(methods::slot(obj1, "ROI"), methods::slot(obj2, "ROI"))
+    tile.metadata <- rbind_metadata(methods::slot(obj1, "tile"), methods::slot(obj2, "tile"))
+    combined.metadata <- methods::new("vrMetadata", 
+                                      molecule = mol.metadata, 
+                                      cell = cell.metadata, 
+                                      spot = spot.metadata, 
+                                      ROI = roi.metadata, 
+                                      tile = tile.metadata)
+  }
+
+  # return combined object
+  return(combined.metadata)
+}
+
+#' Merging vrMetadata objects
+#'
+#' Given a vrMetadata object, and a list of vrMetadata objects, merge all.
+#'
+#' @param x a vrMetadata object
+#' @param y a single or a list of vrMetadata objects
+#'
+#' @method merge vrMetadata
+#'
+#' @importFrom dplyr bind_rows
+#' @importFrom methods slot
+#' @export
+setMethod("merge", "vrMetadata", mergevrMetadata)
+
+#' rbind_metadata
+#'
+#' @param metadata1 metadata1
+#' @param metadata2 metadata2
+#'
+#' @method merge vrMetadata
+#'
+#' @importFrom dplyr bind_rows
+#' @noRd
+#'
+rbind_metadata <- function(metadata1, metadata2){
+  flag1 <- FALSE
+  flag2 <- FALSE
+  if(!inherits(metadata1, "DataFrame")){
+    flag1 <- TRUE
+  }
+  if(!inherits(metadata2, "DataFrame")){
+    flag2 <- TRUE
+  }
+  if(flag1 && flag2){
+    return(dplyr::bind_rows(metadata1,metadata2))
+  } else {
+    if(flag1)
+      metadata1 <- S4Vectors::DataFrame(metadata1)
+    if(flag2)
+      metadata2 <- S4Vectors::DataFrame(metadata2)
+    return(rbind(metadata1, metadata2))
+  }
+}
+
+#' subset_metadata
+#'
+#' @param metadata metadata
+#' @param samples the set of samples to subset the object
+#' @param assays assay name (exp: Assay1), see \code{SampleMetadata(object)}
+#' @param assaytypes assay class (exp: Visium, Xenium), see \code{SampleMetadata(object)}
+#' @param spatialpoints the set of spatial points to subset the object
+#'
+#' @noRd
+subset_metadata <- function(metadata, assays = NULL, assaytypes = NULL, samples = NULL, spatialpoints = NULL){
+  
+  if(inherits(metadata, "data.table")){
+    if(nrow(metadata) > 0){
+      if(!is.null(assays)){
+        metadata <- subset(metadata, subset = assay_id %in% assays)
+      } else if(!is.null(assaytypes)){
+        metadata <- subset(metadata, subset = Assay %in% assaytypes)
+      } else if(!is.null(samples)){
+        metadata <- subset(metadata, subset = Sample %in% samples)
+      } else if(!is.null(spatialpoints)){
+        metadata <- subset(metadata, subset = id %in% spatialpoints)
+      } else {
+        stop("No assay, sample or spatial points were provided!")
+      }  
+    } else {
+      metadata <- data.table::data.table()
+    }
+  } else if(inherits(metadata, "DataFrame")){
+    if(!is.null(assays)){
+      if("assay_id" %in% colnames(metadata)){
+        cur_column <- as.vector(metadata$assay_id)
+        metadata <- metadata[cur_column %in% assays,]
+      } else {
+        cur_column <- as.vector(metadata$id)
+        metadata <- metadata[stringr::str_extract(cur_column, "Assay[0-9]+") %in% assays, ]
+      }
+    } else if(!is.null(assaytypes)){
+      cur_column <- as.vector(metadata$Assay)
+      metadata <- metadata[cur_column %in% assaytypes,]
+    } else if(!is.null(samples)){
+      cur_column <- as.vector(metadata$Sample)
+      metadata <- metadata[cur_column %in% samples,]
+    } else if(!is.null(spatialpoints)){
+      cur_column <- as.vector(metadata$id)
+      metadata <- metadata[cur_column %in% spatialpoints,]
+    } else {
+      stop("No assay, sample or spatial points were provided!")
+    }  
+  } else {
+    if(nrow(metadata) > 0){
+      if(!is.null(assays)){
+        if(!is.null(rownames(metadata))){
+          metadata <- metadata[stringr::str_extract(rownames(metadata), "Assay[0-9]+") %in% assays, ]
+        } else {
+          if("assay_id" %in% colnames(metadata)){
+            metadata <- subset(metadata, subset = assay_id %in% assays)
+          } else {
+            metadata <- metadata[stringr::str_extract(metadata$id, "Assay[0-9]+") %in% assays, ]
+          }
+        }
+      } else if(!is.null(assaytypes)){
+        metadata <- subset(metadata, subset = Assay %in% assaytypes)
+      } else if(!is.null(samples)){
+        metadata <- subset(metadata, subset = Sample %in% samples)
+      } else if(!is.null(spatialpoints)){
+        if(!is.null(rownames(metadata))){
+          metadata <- metadata[rownames(metadata) %in% spatialpoints,]
+        } else {
+          metadata <- metadata[metadata$id %in% spatialpoints,]
+        }
+      } else {
+        stop("No assay, sample or spatial points were provided!")
+      }  
+    }
+  }
+  metadata
+}
+
+#' merge.sampleMetadata
+#'
+#' Merging sample.metadata from two VoltRon objects
+#'
+#' @param metadata_list a list of sample metadata of a VoltRon object
+#'
+#' @noRd
+#'
+merge_sampleMetadata <- function(metadata_list) {
+
+  sample_names <- NULL
+  sample.metadata <- do.call(rbind, metadata_list)
+  rownames(sample.metadata) <- paste0("Assay", seq_len(nrow(sample.metadata)))
+
+  # change sample names if provided
+  if(!is.null(sample_names)){
+
+    # check the number sample names
+    if(!length(sample_names) %in% c(1,nrow(sample.metadata))){
+      stop("Please provide only one sample name or of length of object list!")
+    } else {
+      sample.metadata$Sample <- sample_names
+      section_ids <- rep(NA,nrow(sample.metadata))
+      uniq_names <- unique(sample.metadata$Sample)
+      for(i in seq_len(length(uniq_names))){
+        cur_ind <- which(sample.metadata$Sample == uniq_names[i])
+        section_ids[cur_ind] <- seq_len(length(cur_ind))
+      }
+      sample.metadata$Layer <- paste0("Section", section_ids)
+    }
+  }
+  sample.metadata
+}
+
+### Assay Methods ####
+
+addAssayvrMetadata <- function(object, metadata = NULL, assay, assay_name, sample = "Sample1", layer = "Section1"){
+
+  # get metadata and other info
+  assay.type <- vrAssayTypes(assay)
+  object_metadata <- methods::slot(object, name = assay.type)
+  data <- vrData(assay, norm = FALSE)
+
+  # add new assay
+  assay_ids <- vrAssayNames(object)
+  assay_ids <- as.numeric(gsub("Assay", "", assay_ids))
+  assay_id <- paste0("Assay", max(assay_ids)+1)
+
+  # metadata
+  if(inherits(metadata, "data.table")){
+
+    if(!is.null(metadata)){
+
+      if(nrow(data) > 0){
+        assay_metadata <- data.table::data.table(metadata[, "id", with=FALSE], assay_id = assay_id, Count = Matrix::colSums(data),
+                                                 Assay = assay_name, Layer = layer, Sample = sample,
+                                                 metadata[, colnames(metadata)[!colnames(metadata) %in% c("id", "assay_id", "Count", "Assay", "Layer", "Sample")], with=FALSE])
+      } else{
+        assay_metadata <- data.table::data.table(metadata[, "id", with=FALSE], assay_id = assay_id,
+                                                 Assay = assay_name, Layer = layer, Sample = sample,
+                                                 metadata[, colnames(metadata)[!colnames(metadata) %in% c("id", "assay_id", "Count", "Assay", "Layer", "Sample")], with=FALSE])
+      }
+
+    }
+  } else {
+
+    # get original names
+    entityID_nopostfix <- stringr::str_replace(vrSpatialPoints(assay), pattern = "_Assay[0-9]+", "")
+    entityID <- stringr::str_replace(entityID_nopostfix, pattern = "$", paste0("_", assay_id))
+
+    # if original metadata has rownames
+    if(!"id" %in% colnames(object_metadata)){
+      rownames_metadata <- stringr::str_replace(rownames(metadata), pattern = "_Assay[0-9]+", "")
+      
+      # initiate metadata
+      if(nrow(data) > 0){
+        assay_metadata <- data.frame(Count = Matrix::colSums(data), row.names = entityID)
+      } else {
+        assay_metadata <- data.frame(row.names = entityID)
+      }
+
+      # add metadata
+      if(!is.null(metadata)){
+        if(length(setdiff(rownames_metadata, entityID_nopostfix)) > 0){
+          stop("Some spatial points in the metadata does not match with the assay!")
+        } else{
+          assay_metadata <- dplyr::bind_cols(assay_metadata,
+                                             metadata[,!colnames(metadata) %in% c("Count", "Assay", "Layer", "Sample"), drop = FALSE])
+        }
+      }
+      
+      # complete assay_metadata
+      assay_metadata <- dplyr::bind_cols(data.frame(Assay = rep(assay_name, length(entityID)),
+                                                    Layer = rep(layer, length(entityID)),
+                                                    Sample = rep(sample, length(entityID))),
+                                         assay_metadata)
+    } else {
+      metadata_id <- stringr::str_replace(as.vector(metadata$id), pattern = "_Assay[0-9]+", "")
+      
+      # initiate metadata
+      if(nrow(data) > 0){
+        assay_metadata <- data.frame(id = entityID, Count = Matrix::colSums(data), assay_id = assay_id)
+      } else {
+        assay_metadata <- data.frame(id = entityID, assay_id = assay_id)
+      }
+      
+      # check rownames
+      if(!is.null(rownames(object_metadata))){
+        rownames(assay_metadata) <- assay_metadata$id
+      }
+      
+      # add metadata
+      if(!is.null(metadata)){
+        if(length(setdiff(metadata_id, entityID_nopostfix)) > 0){
+          stop("Some spatial points in the metadata does not match with the assay!")
+        } else{
+          assay_metadata <- dplyr::bind_cols(assay_metadata,
+                                             data.frame(Assay = rep(assay_name, length(entityID)),
+                                                        Layer = rep(layer, length(entityID)),
+                                                        Sample = rep(sample, length(entityID))),
+                                             metadata[,!colnames(metadata) %in% c("id", "Count", "assay_id", "Assay", "Layer", "Sample"), drop = FALSE])
+        }
+      } else {
+        assay_metadata <- dplyr::bind_cols(assay_metadata,
+                                           data.frame(Assay = rep(assay_name, length(entityID)),
+                                                      Layer = rep(layer, length(entityID)),
+                                                      Sample = rep(sample, length(entityID))))
+      }
+    }
+  }
+
+  # add to the main metadata
+  if(inherits(object_metadata, "DataFrame")){
+    object_metadata <- rbind(object_metadata, assay_metadata)
+  } else {
+    object_metadata <- dplyr::bind_rows(object_metadata, assay_metadata)
+  }
+  methods::slot(object, name = assay.type) <- object_metadata
+
+  # return
+  return(object)
+}
+
+#' @rdname addAssay
+#' @method addAssay vrMetadata
+#'
+#' @importFrom dplyr bind_rows bind_cols
+#' @importFrom methods slot slot<-
+#' @importFrom stringr str_replace
+#' @importFrom data.table data.table
+#' @importFrom Matrix colSums
+#'
+#' @export
+setMethod("addAssay", "vrMetadata", addAssayvrMetadata)
+
+vrAssayNamesvrMetadata <- function(object){
+  
+  # get assay names from metadata
+  assay_names <- NULL
+  for(sl in methods::slotNames(object)){
+    cur_metadata <- slot(object, name = sl)
+    if(sl %in% c("molecule", "tile")){
+      cur_names <- cur_metadata$assay_id
+    } else {
+      if("assay_id" %in% colnames(cur_metadata)){
+        cur_names <- as.vector(cur_metadata$assay_id)
+      } else if(!is.null(rownames(cur_metadata))){
+        cur_names <- stringr::str_extract(rownames(cur_metadata), "Assay[0-9]+")
+      } else{
+        cur_names <- stringr::str_extract(as.vector(cur_metadata$id), "Assay[0-9]+")
+      }
+    }
+    assay_names <- c(assay_names, unique(cur_names))
+  }
+  assay_names
+}
+
+#' @rdname vrAssayNames
+#' @order 3
+#' @importFrom methods slotNames
+#' @export
+setMethod("vrAssayNames", "vrMetadata", vrAssayNamesvrMetadata)
+
+#' updateMetadataAssay
+#'
+#' Updating assay names for merge
+#'
+#' @param object1 vrMetadata object
+#' @param object2 vrMetadata object
+#'
+#' @importFrom stringr str_extract
+#' @importFrom methods new
+#'
+#' @noRd
+updateMetadataAssay <- function(object1, object2){
+
+  # get assay types
+  object_list <- slotToList(object1)
+  assaytype <- unlist(lapply(object_list, function(obj) {
+    if(inherits(obj, "data.table")){
+      unique(obj$assay_id)
+    } else if(inherits(obj, c("HDF5DataFrame", "ZarrDataFrame", "DataFrame"))){
+      if("assay_id" %in% colnames(obj)){
+        unique(as.vector(obj$assay_id))
+      } else {
+        unique(stringr::str_extract(as.vector(obj$id), "Assay[0-9]+$"))
+      }
+    } else {
+      unique(stringr::str_extract(rownames(obj), "Assay[0-9]+$"))
+    }
+  }))
+  assaytype <- assaytype[order(nchar(assaytype), assaytype)]
+
+  # replace assay names
+  replacement <- paste0("Assay", seq_len(length(assaytype)))
+  object1 <- lapply(object_list, function(obj) {
+    if(nrow(obj) > 0){
+      
+      if(inherits(obj, "data.table")){
+        
+        # change assay id
+        temp <- obj$assay_id
+        for(i in seq_len(length(assaytype)))
+          temp[grepl(assaytype[i], obj$assay_id)] <- replacement[i]
+        obj$assay_id <- temp
+        return(obj)
+        
+      } else if(inherits(obj, c("HDF5DataFrame", "ZarrDataFrame", "DataFrame"))){
+        
+        # change assay id
+        if("assay_id" %in% colnames(obj)){
+          temp <- as.vector(obj$assay_id)
+          for(i in seq_len(length(assaytype)))
+            temp[grepl(assaytype[i], obj$assay_id)] <- replacement[i]
+          obj$assay_id <- temp
+        }
+        
+        # change id
+        temp <- as.vector(obj$id)
+        for(i in seq_len(length(assaytype))){
+          temp[grepl(paste0(assaytype[i],"$"), obj$id)] <- 
+            gsub(paste0(assaytype[i],"$"), replacement[i],
+                 obj$id[grepl(paste0(assaytype[i],"$"),  obj$id)])
+        }
+        obj$id <- temp
+        
+        return(obj)
+      } else {
+        
+        # change rownames
+        temp <- rownames(obj)
+        for(i in seq_len(length(assaytype)))
+          temp[grepl(paste0(assaytype[i],"$"), rownames(obj))] <- 
+            gsub(paste0(assaytype[i],"$"), replacement[i],
+                 rownames(obj)[grepl(paste0(assaytype[i],"$"), rownames(obj))])
+        rownames(obj) <- temp
+        
+        # change assay id
+        if("assay_id" %in% colnames(obj)){
+          temp <- obj$assay_id
+          for(i in seq_len(length(assaytype)))
+            temp[grepl(assaytype[i], obj$assay_id)] <- replacement[i]
+          obj$assay_id <- temp
+        }
+        return(obj)
+      }
+    } else {
+      return(obj)
+    }
+  })
+  object1 <- methods::new("vrMetadata", 
+                          molecule = object1$molecule, 
+                          cell = object1$cell, 
+                          spot = object1$spot, 
+                          ROI = object1$ROI, 
+                          tile = object1$tile)
+
+  # get assay types
+  object_list <- slotToList(object2)
+  assaytype <- unlist(lapply(object_list, function(obj) {
+    if(inherits(obj, "data.table")){
+      unique(obj$assay_id)
+    } else if(inherits(obj, c("HDF5DataFrame", "ZarrDataFrame", "DataFrame"))){
+      if("assay_id" %in% colnames(obj)){
+        unique(as.vector(obj$assay_id))
+      } else {
+        unique(stringr::str_extract(as.vector(obj$id), "Assay[0-9]+$"))
+      }
+    } else {
+      unique(stringr::str_extract(rownames(obj), "Assay[0-9]+$"))
+    }
+  }))
+  assaytype <- assaytype[order(nchar(assaytype), assaytype)]
+
+  # replace assay names
+  replacement <- paste0("Assay", (length(replacement)+1):(length(replacement) + length(assaytype)))
+  object2 <- lapply(object_list, function(obj) {
+    if(nrow(obj) > 0){
+      if(inherits(obj, "data.table")){
+        
+        # change assay id
+        temp <- obj$assay_id
+        for(i in seq_len(length(assaytype)))
+          temp[grepl(assaytype[i], obj$assay_id)] <- replacement[i]
+        obj$assay_id <- temp
+        
+        return(obj)
+      } else if(inherits(obj, c("HDF5DataFrame", "ZarrDataFrame", "DataFrame"))){
+        
+        # change assay id
+        if("assay_id" %in% colnames(obj)){
+          temp <- as.vector(obj$assay_id)
+          for(i in seq_len(length(assaytype)))
+            temp[grepl(assaytype[i], obj$assay_id)] <- replacement[i]
+          obj$assay_id <- temp
+        }
+        
+        # change id
+        temp <- as.vector(obj$id)
+        for(i in seq_len(length(assaytype))){
+          temp[grepl(paste0(assaytype[i],"$"), obj$id)] <- 
+            gsub(paste0(assaytype[i],"$"), replacement[i], 
+                 obj$id[grepl(paste0(assaytype[i],"$"), obj$id)])
+        }
+        obj$id <- temp
+        
+        return(obj)
+      } else {
+        
+        # change row names
+        temp <- rownames(obj)
+        for(i in seq_len(length(assaytype)))
+          temp[grepl(paste0(assaytype[i],"$"), rownames(obj))] <- 
+            gsub(paste0(assaytype[i],"$"), replacement[i],
+                 rownames(obj)[grepl(paste0(assaytype[i],"$"), rownames(obj))])
+        rownames(obj) <- temp
+        
+        # change id
+        temp <- obj$id
+        for(i in seq_len(length(assaytype))){
+          temp[grepl(paste0(assaytype[i],"$"), obj$id)] <- 
+            gsub(paste0(assaytype[i],"$"), replacement[i], 
+                 obj$id[grepl(paste0(assaytype[i],"$"), obj$id)])
+        }
+        obj$id <- temp
+        
+        # change assay id
+        if("assay_id" %in% colnames(obj)){
+          temp <- obj$assay_id
+          for(i in seq_len(length(assaytype)))
+            temp[grepl(assaytype[i], obj$assay_id)] <- replacement[i]
+          obj$assay_id <- temp
+        }
+        obj
+      }
+    } else {
+      return(obj)
+    }
+  })
+  object2 <- methods::new("vrMetadata", 
+                          molecule = object2$molecule, 
+                          cell = object2$cell, 
+                          spot = object2$spot, 
+                          ROI = object2$ROI, 
+                          tile = object2$tile)
+
+  # return
+  return(list(object1 = object1, object2 = object2))
+}
+
+changeSampleNamesvrMetadata <- function(object, sample_metadata_table){
+
+  # get old and new samples
+  old.samples <- sample_metadata_table$Sample
+  new.samples <- sample_metadata_table$NewSample
+
+  # check all types in the vrMetadata object
+  new_object <- object
+  all_types <- methods::slotNames(object)
+  for(type in all_types){
+    metadata <- methods::slot(object, name = type)
+    new_metadata <-  methods::slot(new_object, name = type)
+    if(nrow(new_metadata) > 0){
+
+      # change samples
+      for(i in seq_len(length(old.samples)))
+        new_metadata$Sample[new_metadata$Sample==old.samples[i]] <- new.samples[i]
+
+      # change layers
+      for(i in seq_len(nrow(sample_metadata_table))){
+        new_metadata$Layer[grepl(paste0(sample_metadata_table$AssayID[i], "$"), rownames(new_metadata))] <- sample_metadata_table[sample_metadata_table$AssayID[i], "NewLayer"]
+      }
+
+      # rewrite metadata type
+      methods::slot(new_object, name = type) <- new_metadata
+    }
+  }
+
+  # return
+  return(new_object)
+}
+
+#' changeSampleNames.vrMetadata
+#'
+#' Change the sample names of the vrMetadata object and reorient layers if needed
+#' This functions requires the new and old sample and layer names passed from \code{changeSampleNames.VoltRon}
+#'
+#' @param sample_metadata_table the sample metadata with old and new layers and samples passed from \code{changeSampleNames.VoltRon}
+#' 
+#' @rdname changeSampleNames
+#' @method changeSampleNames vrMetadata
+#'
+#' @importFrom methods slot slot<- slotNames
+#'
+#' @noRd
+setMethod("changeSampleNames", "vrMetadata", changeSampleNamesvrMetadata)
+
+### Sample Methods ####
+
+vrSampleNamesvrMetadata <- function(object){
+  
+  # get assay names from metadata
+  sample_names <- NULL
+  for(sl in methods::slotNames(object)){
+    cur_metadata <- slot(object, name = sl)
+    sample_names <- c(sample_names, unique(cur_metadata$Sample))
+  }
+  
+  # return
+  sample_names
+}
+
+#' @rdname vrSampleNames
+#' @method vrSampleNames vrMetadata
+#'
+#' @importFrom methods slotNames
+#' @export
+setMethod("vrSampleNames", "vrMetadata", vrSampleNamesvrMetadata)
+
+####
+# Functions ####
+####
+
+#' setVRMetadata
+#'
+#' @param molecule molecule data frame
+#' @param cell cell data frame
+#' @param spot spot data frame
+#' @param ROI ROI data frame
+#' @param tile tile data frame
+#'
+#' @importFrom methods new
+#'
+#' @noRd
+setVRMetadata <- function(metadata, data, entityID, main.assay, assay.type, sample_name, layer_name, version){
+  
+  if(is.null(metadata)){
+
+    # set metadata
+    vr_metadata <- list(molecule = data.table::data.table(),
+                        cell = data.frame(),
+                        spot = data.frame(),
+                        ROI = data.frame(),
+                        tile = data.table::data.table())
+
+    # create entity IDs using Assay index, make it colnames
+    entityID <- stringr::str_replace(entityID, pattern = "$", paste0("_Assay1"))
+
+    # create metadata
+    # slot(vr_metadata, name = assay.type) <-
+    if(version == "v1"){
+      vr_metadata[[assay.type]] <- 
+        data.frame(Count = Matrix::colSums(data),
+                   assay_id = "Assay1",
+                   Assay = main.assay,
+                   Layer = layer_name,
+                   Sample = sample_name,
+                   row.names = entityID) 
+    } else if (version == "v2"){
+      vr_metadata[[assay.type]] <- 
+        data.frame(id = entityID,
+                   Count = Matrix::colSums(data),
+                   assay_id = "Assay1",
+                   Assay = main.assay,
+                   Layer = layer_name,
+                   Sample = sample_name,
+                   row.names = entityID) 
+    }
+
+  } else {
+    if(any(is(metadata) %in% c("data.table", "data.frame", "matrix"))){
+      vr_metadata <- list(molecule = data.table::data.table(),
+                          cell = data.frame(),
+                          spot = data.frame(),
+                          ROI = data.frame(),
+                          tile = data.table::data.table())
+
+      # if metadata is a data.table
+      if(inherits(metadata, "data.table")){
+
+        # if there are no id column, insert entityID
+        if(!"id" %in% colnames(metadata)){
+          metadata$id <- entityID  
+        }
+        
+        # check ID names
+        if(length(setdiff(metadata$id, entityID)) > 0){
+          stop("Entity IDs are not matching")
+        } else {
+
+          # entity IDs
+          metadata <- subset(metadata, subset = entityID %in% id)
+
+          # create entity IDs using Assay index, make it colnames
+          set.seed(nrow(metadata$id))
+          entityID <- paste0(metadata$id, "_", ids::random_id(bytes = 3, use_openssl = FALSE))
+
+          if(nrow(data) > 0){
+            suppressWarnings({
+              vr_metadata[[assay.type]] <-
+                data.table::data.table(id = entityID,
+                                       assay_id = "Assay1",
+                                       Count = Matrix::colSums(data),
+                                       Assay = main.assay,
+                                       Layer = layer_name,
+                                       Sample = sample_name,
+                                       metadata[,-"id"])
+            })
+          } else{
+            suppressWarnings({
+              vr_metadata[[assay.type]] <-
+                  data.table::data.table(id = entityID,
+                                         assay_id = "Assay1",
+                                         Assay = main.assay,
+                                         Layer = layer_name,
+                                         Sample = sample_name, 
+                                         metadata[,-"id"])
+            })
+          }
+        }
+
+      # if metadata is a regular data.frame
+      } else if(inherits(metadata, "data.frame")){
+
+        # check row names
+        if(length(setdiff(rownames(metadata), entityID)) > 0){
+          stop("Entity IDs are not matching")
+        } else {
+
+          # entity IDs
+          if(version == "v1") {
+            metadata <- metadata[entityID,] 
+          } else if(version == "v2") {
+            
+            # if there are no id column, insert entityID
+            if(!"id" %in% colnames(metadata)){
+              metadata$id <- entityID  
+            }
+            metadata <- metadata[match(entityID, metadata$id),]
+          }
+
+          # create entity IDs using Assay index, make it colnames
+          entityID <- stringr::str_replace(entityID, pattern = "$", paste0("_Assay1"))
+
+          # create metadata for version 1
+          if(version == "v1"){
+            if(nrow(data) > 0){
+              vr_metadata[[assay.type]] <-
+                data.frame(Count = Matrix::colSums(data),
+                           assay_id = "Assay1",
+                           Assay = main.assay,
+                           Layer = layer_name,
+                           Sample = sample_name,
+                           metadata, 
+                           row.names = entityID)
+            } else{
+              vr_metadata[[assay.type]] <-
+                data.frame(assay_id = "Assay1",
+                           Assay = main.assay,
+                           Layer = layer_name,
+                           Sample = sample_name,
+                           metadata,
+                           row.names = entityID)
+            } 
+          
+          # create metadata for version 2
+          } else if(version == "v2"){
+            if(nrow(data) > 0){
+              vr_metadata[[assay.type]] <-
+                data.frame(id = entityID,
+                           Count = Matrix::colSums(data),
+                           assay_id = "Assay1",
+                           Assay = main.assay,
+                           Layer = layer_name,
+                           Sample = sample_name,
+                           metadata, 
+                           row.names = entityID)
+            } else{
+              vr_metadata[[assay.type]] <-
+                data.frame(id = entityID,
+                           Assay = main.assay,
+                           assay_id = "Assay1",
+                           Layer = layer_name,
+                           Sample = sample_name,
+                           metadata,
+                           row.names = entityID)
+            }
+          }
+          
+        }
+      }
+    }
+  }
+  
+  return(
+    list(
+      entityID = entityID,
+      vr_metadata =  methods::new("vrMetadata", 
+                                 molecule = vr_metadata$molecule, 
+                                 cell = vr_metadata$cell, 
+                                 spot = vr_metadata$spot, 
+                                 ROI = vr_metadata$ROI, 
+                                 tile = vr_metadata$tile)
+    )
+  )
+}
+
+#' setVRSampleMetadata
+#'
+#' @param samples a list of vrSample object
+#'
+#' @noRd
+setVRSampleMetadata <- function(samples){
+
+  # imput missing sample names
+  # sample_name_ind <- sapply(names(samples), is.null)
+  sample_name_ind <- vapply(names(samples), is.null, logical(1))
+  if(length(sample_name_ind) > 0){
+    names_samples <- names(samples)
+    if(any(sample_name_ind)){
+      null_samples_ind <- which(sample_name_ind)
+      names_samples[null_samples_ind] <- paste0("Sample", null_samples_ind)
+    }
+  } else {
+    names_samples <- paste0("Sample", seq_len(length(samples)))
+  }
+
+  # get sample metadata
+  sample_list <- names(samples)
+  sample.metadata <- NULL
+  for(i in seq_len(length(sample_list))){
+    layer_list <- samples[[sample_list[i]]]@layer
+    layer_data <- NULL
+    for(j in seq_len(length(layer_list))){
+      assay_list <- layer_list[[j]]@assay
+      layer_data <- rbind(layer_data, cbind(names(assay_list), names(layer_list)[j]))
+    }
+    sample.metadata <- rbind(sample.metadata, cbind(layer_data, sample_list[i]))
+  }
+  sample.metadata <- data.frame(sample.metadata, row.names = paste0("Assay", seq_len(nrow(sample.metadata))))
+  colnames(sample.metadata) <- c("Assay", "Layer", "Sample")
+
+  sample.metadata
+}