some clarifications

[aleednn]

• How can I get the barcodes present in each subclone? (tsne_CNA graph)
• tsne_CNA graph is done only on tumor cells?

Thank you!

[AntonioDeFalco]

Hi @aleednn,

• How can I get the barcodes present in each subclone? (tsne_CNA graph)

The pipeline outputs a data.frame with this information as well, as shown in the vignette.

results <- pipelineCNA

• tsne_CNA graph is done only on tumor cells?

Yes, only on tumor cells.

Regards

[aleednn]

Thank you @AntonioDeFalco for your reply.

i used:
results <- pipelineCNA(count_mtx, norm_cell = listNormCells, sample = "pt", par_cores = 25, SUBCLONES = TRUE, plotTree = TRUE)

but the value of confidential_normal in results is always "yes" for both tumor and non-tumor cells.

What could be the problem?

Regards.