supercell_GE: Simplification of scRNA-seq dataset

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

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
)

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)

Value

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

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