bseqsc_basis: Building a Basis Matrix of Reference Gene Expression Profiles

In shenorrLab/bseqsc: Deconvolution of Bulk Sequencing Experiments using Single Cell Data

Description

Building a Basis Matrix of Reference Gene Expression Profiles

Usage

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.

shenorrLab/bseqsc documentation built on May 29, 2019, 9:23 p.m.