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Error at oncoHeat step for subclones #74

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smdn-tt opened this issue Sep 14, 2023 · 1 comment
Open

Error at oncoHeat step for subclones #74

smdn-tt opened this issue Sep 14, 2023 · 1 comment

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@smdn-tt
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smdn-tt commented Sep 14, 2023

Greetings and thanks for this amazing package!
I have been running SCEVAN v1.0.1 on a number of snRNA samples, and after proceeding through the first 7 without issue I received this error message on the 8th sample. I can't spot what is different between this sample and the other cases, so would appreciate any help in interpreting this error or why there may be an empty value/dimension.

Many thanks
Sol

[1] "found 7028 tumor cells"
[1] "time classify tumor cells: 3.06953304304017"
[1] "found 7 subclones"
percentage_cells_subsclone_1 percentage_cells_subsclone_2
0.16021628 0.19721116
percentage_cells_subsclone_3 percentage_cells_subsclone_4
0.11582242 0.06829824
percentage_cells_subsclone_5 percentage_cells_subsclone_6
0.10145134 0.14854866
percentage_cells_subsclone_7
0.20845191
[1] "Segmentation of subclone : 1"
[1] "Segmentation of subclone : 2"
[1] "Segmentation of subclone : 3"
[1] "Segmentation of subclone : 4"
[1] "Segmentation of subclone : 5"
[1] "Segmentation of subclone : 6"
[1] "Segmentation of subclone : 7"
$OS8A_clone
Chr Start End Alteration segm.mean
26 12 57475445 96400560 2 0.292804

Error in apply(oncoHeat[-sub, ], 1, function(x) sum(oncoHeat[sub, ] == :
dim(X) must have a positive length
Calls: pipelineCNA -> subcloneAnalysisPipeline -> apply
In addition: Warning message:
In annoteBandOncoHeat(res_proc$count_mtx_annot, diffSubcl, res_subclones$n_subclones, :
NAs introduced by coercion
Execution halted

@zhangli-tools
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I encountered the same issue. It seems that 'oncoHeat' is not a matrix but rather a vector

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