Feature selection

No feature selection step

Deconvolution

For the ICA-based deconvolution step, the function fastICA::fastICA is run with the parameters n.comp = k, maxit = 1000 and tol = 1e-09, and the remaining parameters set to default.

The 30 most important genes of each ICA component are extracted by the function deconica::generate_markers with the parameter return = “gene.ranked”. These genes are used to weight the components score with the function deconica::get_scores, with the log counts of the ICA as df parameter, the list of 30 genes as markers.list parameter, and the parameter summary = "weighted.mean".

Finally, the proportions are computed using the absolute value of the weighted scores.

Results

The program returns an estimated proportion matrix and the corresponding estimated cell-type specific profiles matrix.

Descriptors

Omics_type = trancriptome and methylome

Cancer_type = all

Method_type = unsupervised

Cell_type = all