View source: R/Deconvolution.R
SCDC_prop_ONE_subcl_marker | R Documentation |
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, ... )
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'. |
Estimated proportion, basis matrix, predicted gene expression levels for bulk samples
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