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!