updateMarkers: Update cellMarkers object

In cellGeometry: Geometric Single Cell Deconvolution

Update cellMarkers object

Description

Updates a 'cellMarkers' gene signature object with new settings without having to rerun calculation of gene means, which can be slow.

Usage

updateMarkers(
  object = NULL,
  genemeans = NULL,
  groupmeans = NULL,
  add_gene = NULL,
  add_groupgene = NULL,
  remove_gene = NULL,
  remove_groupgene = NULL,
  remove_subclass = NULL,
  remove_group = NULL,
  bulkdata = NULL,
  nsubclass = object$opt$nsubclass,
  ngroup = object$opt$ngroup,
  expfilter = object$opt$expfilter,
  noisefilter = object$opt$noisefilter,
  noisefraction = object$opt$noisefraction,
  verbose = TRUE
)

Arguments

object	A 'cellMarkers' class object. Either object or genemeans must be specified.
genemeans	A matrix of mean gene expression with genes in rows and cell subclasses in columns.
groupmeans	Optional matrix of mean gene expression for overarching main cell groups (genes in rows, cell groups in columns).
add_gene	Character vector of gene markers to add manually to the cell subclass gene signature.
add_groupgene	Character vector of gene markers to add manually to the cell group gene signature.
remove_gene	Character vector of gene markers to manually remove from the cell subclass gene signature.
remove_groupgene	Character vector of gene markers to manually remove to the cell group gene signature.
remove_subclass	Character vector of cell subclasses to remove.
remove_group	Optional character vector of cell groups to remove.
bulkdata	Optional data matrix containing bulk RNA-Seq data with genes in rows. This matrix is only used for its rownames, to ensure that cell markers are selected from genes in the bulk dataset.
nsubclass	Number of genes to select for each single cell subclass. Either a single number or a vector with the number of genes for each subclass.
ngroup	Number of genes to select for each cell group.
expfilter	Genes whose maximum mean expression on log2 scale per cell type are below this value are removed and not considered for the signature.
noisefilter	Sets an upper bound for noisefraction cut-off below which gene expression is set to 0. Essentially gene expression above this level must be retained in the signature. Setting this higher can allow more suppression via noisefraction and can favour more highly expressed genes.
noisefraction	Numeric value. Maximum mean log2 gene expression across cell types is calculated and values in celltypes below this fraction are set to 0. Set in conjunction with noisefilter. Note: if this is set too high (too close to 1), it can have a deleterious effect on deconvolution.
verbose	Logical whether to show messages.

Value

A list object of S3 class 'cellMarkers'. See cellMarkers() for details. If gene2symbol() has been called, an extra list element symbol will be present. The list element update stores the call to updateMarkers().

Author(s)

Myles Lewis

See Also

cellMarkers() gene2symbol()

cellGeometry documentation built on April 20, 2026, 1:06 a.m.