normaliseExprs: normaliseExprs

In SydneyBioX/CiteFuse: CiteFuse: multi-modal analysis of CITE-seq data

normaliseExprs

Description

A function that perform normalisation for alternative expression

Usage

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")

SydneyBioX/CiteFuse documentation built on Feb. 13, 2023, 6:04 a.m.