Single cells Clustering QC
my_qc(sc.eset, ct.varname, sample, scsetname = "Single Cell", ct.sub, iter.max = 1000, nu = 1e-04, epsilon = 0.01, arow = NULL, qcthreshold = 0.7, ...)
| sc.eset | ExpressionSet object for single cells |
|---|---|
| ct.varname | variable name for 'cell type' |
| sample | variable name for subject/sample |
| scsetname | the name for the single cell dataset |
| 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 |
| arow | annotation of rows for pheatmap |
| qcthreshold | the probability threshold used to filter out questionable cells |
a list including: 1) a probability matrix for each single cell input; 2) a clustering QCed ExpressionSet object; 3) a heatmap of QC result.