SCDC_prop: Proportion estimation

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

Proportion estimation

Description

Proportion estimation function for multi-subject case

Usage

SCDC_prop(
  bulk.eset,
  sc.eset,
  ct.varname,
  sample,
  ct.sub,
  iter.max = 1000,
  nu = 1e-04,
  epsilon = 0.01,
  truep = NULL,
  weight.basis = T,
  ct.cell.size = NULL,
  Transform_bisque = F,
  ...
)

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
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
truep	true cell-type proportions for bulk samples if known
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.
Transform_bisque	The bulk sample transformation from bisqueRNA. Aiming to reduce the systematic difference between single cells and bulk samples.

Value

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

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