A function that perform normalisation for alternative expression

normaliseExprs(
  sce,
  altExp_name = NULL,
  exprs_value = "counts",
  transform = c("log", "clr", "zi_minMax", "minMax"),
  log_offset = NULL
)

Arguments

sce

A SingleCellExperiment object

altExp_name

Name of alternative expression that will be used to perform normalisation

exprs_value

A character indicates which expression value in assayNames is used.

transform

type of transformation, either log or clr (Centered log ratio transform)

log_offset

Numeric scalar specifying the pseudo-count to add when log-transforming expression values. Default is 1

Value

a SingleCellExperiment object

Examples

data(CITEseq_example, package = "CiteFuse") sce_citeseq <- preprocessing(CITEseq_example) sce_citeseq <- normaliseExprs(sce = sce_citeseq, altExp_name = "ADT", transform = "log")