supercell_merge: Merging independent SuperCell objects

In SuperCell: Simplification of scRNA-Seq Data by Merging Together Similar Cells

Merging independent SuperCell objects

Description

This function merges independent SuperCell objects

Usage

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

Value

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

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 documentation built on Oct. 25, 2024, 5:07 p.m.