normalizeCounts: Normalizes counts to CPM

In JEFworks-Lab/MERINGUE: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities

Normalizes counts to CPM

Description

Normalizes raw counts to log10 counts per million with pseudocount

Usage

normalizeCounts(
  counts,
  normFactor = NULL,
  depthScale = 1e+06,
  pseudo = 1,
  log = TRUE,
  verbose = TRUE
)

Arguments

counts	Read count matrix. The rows correspond to genes, columns correspond to individual cells
normFactor	Normalization factor such as cell size. If not provided column sum as proxy for library size will be used
depthScale	Depth scaling. Using a million for CPM (default: 1e6)
pseudo	Pseudocount for log transform (default: 1)
log	Whether to apply log transform
verbose	Verbosity (default: TRUE)

Value

a normalized matrix

JEFworks-Lab/MERINGUE documentation built on June 8, 2022, 11:41 p.m.