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SuperCell (version 1.0)

supercell_GE: Simplification of scRNA-seq dataset

Description

This function converts (i.e., averages or sums up) gene-expression matrix of single-cell data into a gene expression matrix of metacells

Usage

supercell_GE(
  ge,
  groups,
  mode = c("average", "sum"),
  weights = NULL,
  do.median.norm = FALSE
)

Value

a matrix of simplified (averaged withing groups) data with ncol equal to number of groups and nrows as in the initial dataset

Arguments

ge

gene expression matrix (or any coordinate matrix) with genes as rows and cells as cols

groups

vector of membership (assignment of single-cell to metacells)

mode

string indicating whether to average or sum up `ge` within metacells

weights

vector of a cell weight (NULL by default), used for computing average gene expression withing cluster of metaells

do.median.norm

whether to normalize by median value (FALSE by default)