SCDC_ENSEMBLE: ENSEMBLE function

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

ENSEMBLE function

Description

ENSEMBLE function for deconvolution results output from SCDC_prop.

Usage

SCDC_ENSEMBLE(
  bulk.eset,
  sc.eset.list = NULL,
  ct.varname,
  sample,
  ct.sub,
  grid.search = F,
  search.length = 0.05,
  iter.max = 2000,
  nu = 1e-04,
  epsilon = 0.001,
  truep = NULL,
  weight.basis = T,
  prop.input = NULL,
  Transform_bisque = F,
  ct.cell.size = NULL,
  ...
)

Arguments

bulk.eset	ExpressionSet object for bulk samples
sc.eset.list	list of ExpressionSet objects for single cell reference datasets. Note that the variable names of multiple ExpressionSet objects should be consistent. Not required if prop.input is specified.
ct.varname	character string specifying the variable name for 'cell types'. Not required if prop.input is specified.
sample	character string specifying the variable name for subject/samples. Not required if prop.input is specified.
ct.sub	vector. a subset of cell types that are selected to construct basis matrix. Not required if prop.input is specified.
grid.search	logical. whether to allow grid search method to derive the ENSEMBLE weights.
search.length	a number between 0 to 0.5. if using "Grid search", the step length used. Smaller search.length derives more accurate optimization results.
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
prop.input	A list of SCDC_prop objects. Default is NULL. Users can use the SCDC function CreateSCDCpropObj to create the SCDC_prop objects first, and then put all objects into a list as this input. This allows users to ENSEMBLE results calculated from other deconvolution methods.
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.

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