No tumor cell found in output but tumor cell reported in log

[chenhong-dkfz]

Dear all,

When I run SCEVAN I found it is very strange. Here I see 161 tumor cells found during process but in the result object generated by the function, there is no cell annotated as "tumor". Could you please help? Thank you very much.

cells_to_keep <- rownames(scDataMerged@meta.data[grepl("T11", scDataMerged@meta.data$batch), ])
scDataSubset_T1 <- subset(scDataMerged, cells = cells_to_keep)
results_T1 <- SCEVAN::pipelineCNA(scDataSubset_T1@assays$SCT$counts, par_cores = 4, SUBCLONES = TRUE, plotTree = TRUE, sample="T11")
[1] " raw data - genes: 24310 cells: 257"
[1] "1) Filter: cells > 200 genes"
[1] "2) Filter: genes > 10% of cells"
[1] "13616 genes past filtering"
[1] "3) Annotations gene coordinates"
[1] "found 30 confident non malignant cells"
[1] "12119 genes annotated"
[1] "4) Filter: genes involved in the cell cycle"
[1] "11557 genes past filtering "
[1] "5) Filter: cells > 5genes per chromosome "
[1] "6) Log Freeman Turkey transformation"
[1] "A total of 257 cells, 11557 genes after preprocessing"
[1] "7) Measuring baselines (confident normal cells)"
[1] "8) Smoothing data"
[1] "9) Segmentation (VegaMC)"
[1] "10) Adjust baseline"
[1] "11) plot heatmap"
[1] "found 161 tumor cells"
[1] "time classify tumor cells: 1.73901759783427"
[1] "found 0 subclones"
[1] "time subclones: 0.516113996505737"
table(results_T1$class)

normal
257

table(results_T1$confidentNormal)

yes
30

length(cells_to_keep)
[1] 257