# Merging independent SuperCell objects This function merges independent SuperCell objects ```r supercell_merge(SCs, fields = c()) ``` ## Arguments - `SCs`: list of SuperCell objects (results of SCimplify ) - `fields`: which additional fields (e.g., metadata) of the the SuperCell objects to keep when merging ## Returns a list with components * membership - assignment of each single cell to a particular metacell * cell.ids - the original ids of single-cells * supercell_size - size of metacells (former super-cells) * gamma - graining level of the merged object (estimated as an average size of metacells as the independent SuperCell objects might have different graining levels) * N.SC - number of obtained metacells ## Examples ```r data(cell_lines) # list with GE - gene expression matrix (logcounts), meta - cell meta data GE <- cell_lines$GE cell.meta <- cell_lines$meta cell.idx.HCC827 <- which(cell.meta == "HCC827") cell.idx.H838 <- which(cell.meta == "H838") SC.HCC827 <- SCimplify(GE[,cell.idx.HCC827], # log-normalized gene expression matrix gamma = 20, # graining level n.var.genes = 1000, k.knn = 5, # k for kNN algorithm n.pc = 10) # number of principal components to use SC.HCC827$cell.line <- supercell_assign( cell.meta[cell.idx.HCC827], supercell_membership = SC.HCC827$membership) SC.H838 <- SCimplify(GE[,cell.idx.H838], # log-normalized gene expression matrix gamma = 30, # graining level n.var.genes = 1000, # number of top var genes to use for the dim reduction k.knn = 5, # k for kNN algorithm n.pc = 15) # number of proncipal components to use SC.H838$cell.line <- supercell_assign( cell.meta[cell.idx.H838], supercell_membership = SC.H838$membership) SC.merged <- supercell_merge(list(SC.HCC827, SC.H838), fields = c("cell.line")) # compute metacell gene expression for SC.HCC827 SC.GE.HCC827 <- supercell_GE(GE[, cell.idx.HCC827], groups = SC.HCC827$membership) # compute metacell gene expression for SC.H838 SC.GE.H838 <- supercell_GE(GE[, cell.idx.H838], groups = SC.H838$membership) # merge GE matricies SC.GE.merged <- supercell_mergeGE(list(SC.GE.HCC827, SC.GE.H838)) ```

supercell_merge function