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navinlabcode / copykat

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CNAmat does not contain gene symbol when using genome = "hg20" #90

Open WT215 opened 1 year ago

WT215 commented 1 year ago

Hello,

Thank you for this nice package!

When I use human genes, the output CNAmat does not contain gene symbol. However, when I use genome="mm10", there is a column in CNAmat which stores gene symbol. Why they are different?

I noticed in the note Only difference is that the result is output in gene space instead of genomic space. Meaning the locations of CNVs is labelled by gene names, instead of genomic positions.. Can gene names be added to CNAmat output based on human genome?

Can the heatmap plotting step be omitted? It is time consuming.

Many thanks!

SeadonXing commented 1 year ago

I also want to obtain the final CNA matrix with gene symbols in rows and cell names in columns. In "test_copykat_CNA_raw_results_gene_by_cell.txt" I can find that, but it's not the final CNA matrix for the plot. In "test_copykat_CNA_results.txt", it's the final CNA signal, but miss gene symbols. I agree with @WT215 that the matrix with gene symbols is helpful for doing further analyses. I also agree with @WT215 that the heatmap plotting step is time-consuming, any methods to omit that?