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colomemaria / epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data
GNU General Public License v3.0
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how to control number of sub-clones ? #34

Open Krithika-Bhuvan opened 2 days ago

Krithika-Bhuvan commented 2 days ago

Hello, is there a way to control the number of sub-clones

So far i did this - I wanted to get 2 sub-clones so i set tree_depth=2, but the sub-clone output still gives me clones from 1 - 4 and NA value.

Is there way to control the number of sub-clones output ? Eg: I want 2 sub-clones

subclones <- epiAneufinder::split_subclones(res_table,
                                              tree_depth=2,
                                              plot_tree=TRUE,
                                              plot_path=paste0(sampleCNVpath,"/subclones.pdf"),
                                              plot_width=4,
                                              plot_height=3)
thek71 commented 1 day ago

Hi Krithika,

I think that if you specify the tree depth at 1, then you will get the first two classes. Please try using tree_depth =1 and just tell us if it worked.

Best, Katia