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AntonioDeFalco / SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
https://www.nature.com/articles/s41467-023-36790-9
GNU General Public License v3.0
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Error at oncoHeat step for subclones #74

Open smdn-tt opened 1 year ago

smdn-tt commented 1 year ago

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 commented 10 months ago

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