To identify malignant cells from epithelia, we used the CopyKAT algorithm (version 0.1.0) [20 (link)] to estimate the copy number variations (CNVs). The stromal cells (fibroblasts and endothelia) were used as normal reference, and the parameters were default. The sum of calculated CNV for each gene per cell was defined as the CNV score of the cell.
Free full text: Click here