SCDC_basis: Basis Matrix

In meichendong/SCDC: Bulk RNA-seq deconvolution by scRNA-seq with multi-reference datasets

Basis Matrix

Description

Basis matrix construction

Usage

SCDC_basis(x, ct.sub = NULL, ct.varname, sample, ct.cell.size = NULL)

Arguments

x	ExpressionSet object for single cells
ct.sub	a subset of cell types that are selected to construct basis matrix
ct.varname	variable name for 'cell types'
sample	variable name for subject/samples
ct.cell.size	default is NULL, which means the "library size" is calculated based on the data. Users can specify a vector of cell size factors corresponding to the ct.sub according to prior knowledge. The vector should be named: names(ct.cell.size input) should not be NULL.

Value

a list of basis matrix, sum of cell-type-specific library size, sample variance matrix, basis matrix by mvw, mvw matrix.

meichendong/SCDC documentation built on Jan. 26, 2023, 5:08 p.m.