Building a Basis Matrix of Reference Gene Expression Profiles
bseqsc_basis(x, markers, clusters, samples, ct.scale = TRUE, limit = TRUE)
Arguments
- x
- matrix of raw counts
- markers
- list of cell type marker genes.
The type of gene identifiers must be the same as the ones used as feature/row names in
x.
- clusters
- vector giving the cell type of each cell (i.e. column) in the data
x.
If x is an ExpressionSet object, it can also be the name (as a string) of the
phenotypic variable to use.
- samples
- vector giving the sample of origin of each cell (i.e. column) in the data
x.
If x is an ExpressionSet object, it can also be the name (as a string) of the
phenotypic variable to use.
- ct.scale
- logical that indicates if the single cell expresson profiles
should be rescaled according to their cell type average total count.
- limit
- logical that indicates if the returned basis matrix should only contain
cell types listed in
markers.
Value
a matrix object.