Tree-guided proportion estimation for ONE subject

Proportion estimation function for ONE-subject case, and apply tree-guided deconvolution

SCDC_prop_ONE_subcl_marker(
  bulk.eset,
  sc.eset,
  ct.varname,
  fl.varname,
  sample,
  truep = NULL,
  ct.sub = NULL,
  ct.fl.sub,
  iter.max = 3000,
  nu = 1e-04,
  epsilon = 0.001,
  weight.basis = F,
  bulk_disease = NULL,
  select.marker = T,
  markers = NULL,
  marker.varname = NULL,
  pseudocount.use = 1,
  LFC.lim = 0.5,
  allgenes.fl = F,
  ct.cell.size = NULL,
  fl.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'
fl.varname	variable name for first-level 'meta-clusters'
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
ct.fl.sub	'cell types' for first-level 'meta-clusters'
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
weight.basis	logical, use basis matrix adjusted by MVW, default is T.
select.marker	logical, select marker genes to perform deconvolution in tree-guided steps. Default is T.
markers	A set of marker gene that input manully to be used in deconvolution. If NULL, then
marker.varname	variable name of cluster groups when selecting marker genes. If NULL, then use ct.varname.
pseudocount.use	a constant number used when selecting marker genes, default is 1.
LFC.lim	a threshold of log fold change when selecting genes as input to perform Wilcoxon's test.
allgenes.fl	logical, use all genes in the first-level deconvolution
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.
fl.cell.size	default is NULL, similar to ct.cell.size. This is for first-level 'meta-clusters'.

Value

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