Error in `[.data.frame`(res_class$CNAmat, , res_class$tum_cells) : undefined columns selected

[DGladish]

Hello!

I have just obtained data from a TEA-seq experiment and am trying to run SCEVAN on the extracted gene expression data. I am receiving the following error:

results <- SCEVAN::pipelineCNA(BM4_raw_mat_subset, par_cores = 1, SUBCLONES = TRUE, plotTree = TRUE)
[1] " raw data - genes: 36601 cells: 350"
[1] "1) Filter: cells > 200 genes"
[1] "low data quality"
[1] "2) Filter: genes > 5% of cells"
[1] "7970 genes past filtering"
[1] "3) Annotations gene coordinates"
Warning: package ‘dplyr’ was built under R version 4.3.2
Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
[1] "found 0 confident non malignant cells"
[1] "7212 genes annotated"
[1] "4) Filter: genes involved in the cell cycle"
[1] "6740 genes past filtering "
[1] "5) Filter: cells > 5genes per chromosome "
[1] "6) Log Freeman Turkey transformation"
[1] "A total of 341 cells, 6740 genes after preprocessing"
[1] "7) Measuring baselines (pure tumor - synthetic normal cells)"
[1] "8) Smoothing data"
[1] "10) Adjust baseline"
[1] "11) plot heatmap"
[1] "found 341 tumor cells"
[1] "time classify tumor cells: 2.1086800177892"
Error in [.data.frame(res_class$CNAmat, , res_class$tum_cells) :
undefined columns selected

Any ideas as to why I would be experiencing this? I would appreciate any help :)

Thank you!

[AntonioDeFalco]

Hi @DGladish ,
Can you share an example of a cell name of this matrix, e.g. are there dots in the names?

Thanks