SCDC_prop_ONE: Proportion estimation function for one-subject case

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

Proportion estimation function for one-subject case

Description

Proportion estimation function for one-subject case

Usage

SCDC_prop_ONE(
  bulk.eset,
  sc.eset,
  ct.varname,
  sample,
  truep = NULL,
  ct.sub,
  iter.max = 2000,
  nu = 1e-10,
  epsilon = 0.01,
  weight.basis = T,
  ct.cell.size = NULL,
  ...
)

Arguments

bulk.eset	ExpressionSet object for bulk samples
sc.eset	ExpressionSet object for single cell samples
ct.varname	variable name for 'cell types'
sample	variable name for subject/samples
truep	true cell-type proportions for bulk samples if known
ct.sub	a subset of cell types that are selected to construct basis matrix
iter.max	the maximum number of iteration in WNNLS
nu	a small constant to facilitate the calculation of variance
epsilon	a small constant number used for convergence criteria
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

Estimated proportion, basis matrix, predicted gene expression levels for bulk samples

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