We employed inferCNV57 to estimate copy number variations (CNVs) for the breast cancer ST slices. We used the default setting cut-off = 0.1 for inferCNV, i.e., only genes with an average count > 0.1 were considered. We used spots containing < 10% cancer cells as reference samples and other spots as malignant samples. To compare the CNV values inferred from different slices and different experimental batches, we scaled the inferred CNV values to −1 ~ 1, and we calculated the average inferred CNV at each genomic locus for all spots in a spatial domain, to represent the mutation information of the spatial domain.
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