Proportion estimation function for multi-subject case
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, ... )
| 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. |
Estimated proportion, basis matrix, predicted gene expression levels for bulk samples