Haplotype-aware analysis of somatic copy number variations from single -cell transcriptomes
Extended Data Fig. 3 WGS validation of Numbat CNV calls from scRNA-seq data.
For each sample, the DNA profile is juxtaposed with the copy number profile inferred by the Numbat joint HMM . Gray vertical bars represent centromeres and gap regions. logR, log coverage ratio. BAF, B-allele frequency. logFC, log expression fold-change. pHF, paternal haplotype frequency. BAMP, balanced amplification.
Each dot represents a distinct sample . Center line, mean. ATC5 was excluded from the benchmark due to lack of clear expression of tumor markerThe aneuploidy probability is shown as a color gradient . For each sample , the series of figures respectively show the aneuploidy probabilities by expression evidence, those by allele evidence, those by combined evidence, CopyKAT prediction , and marker gene expression in a t-SNE embedding of gene expression profiles.
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