Updates a 'cellMarkers' gene signature object with new settings without having to rerun calculation of gene means, which can be slow.
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
)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().
A 'cellMarkers' class object. Either object or genemeans
must be specified.
A matrix of mean gene expression with genes in rows and cell subclasses in columns.
Optional matrix of mean gene expression for overarching main cell groups (genes in rows, cell groups in columns).
Character vector of gene markers to add manually to the cell subclass gene signature.
Character vector of gene markers to add manually to the cell group gene signature.
Character vector of gene markers to manually remove from the cell subclass gene signature.
Character vector of gene markers to manually remove to the cell group gene signature.
Character vector of cell subclasses to remove.
Optional character vector of cell groups to remove.
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.
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.
Number of genes to select for each cell group.
Genes whose maximum mean expression on log2 scale per cell type are below this value are removed and not considered for the signature.
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.
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.
Logical whether to show messages.
Myles Lewis
cellMarkers() gene2symbol()