Proportion estimation function for multi-subject case, and apply tree-guided deconvolution
SCDC_prop_subcl_marker( bulk.eset, sc.eset, ct.varname, fl.varname, sample, ct.sub = NULL, ct.fl.sub, iter.max = 3000, nu = 1e-04, epsilon = 0.001, weight.basis = T, truep = NULL, select.marker = T, markers = NULL, marker.varname = NULL, allgenes.fl = F, pseudocount.use = 1, LFC.lim = 0.5, ct.cell.size = NULL, fl.cell.size = NULL, ... )
| 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 |
| 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. |
| truep | true cell-type proportions for bulk samples if known |
| 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. |
| allgenes.fl | logical, use all genes in the first-level deconvolution |
| 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. |
| 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'. |
Estimated proportion, basis matrix, predicted gene expression levels for bulk samples