qc_cells function produces error with the cell-cycle file

[PiStefania]

When executing the function:

cells.df = auto_cna_signal(
  'SAMPLES/sampleA',
  'genes.tsv',
  prefix = 'example',
  cell_cycle = 'cc_genes.tsv',
  use_cache = FALSE
)

using the files:

• sample: one of the samples from SCP, taken from https://singlecell.broadinstitute.org/single_cell/study/SCP393/single-cell-rna-seq-of-adult-and-pediatric-glioblastoma#study-download
• genes.tsv: file produced from your instructions, when downloaded from "ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz"
• cc_genes.tsv: file downloaded from "https://raw.githubusercontent.com/jmonlong/scCNAutils/master/docs/cell-cycle-genes-tirosh2016.tsv"

The error is the following: <error/vctrs_error_subscript_type> Must subset columns with a valid subscript vector. x Subscript has the wrong type rlang_data_pronoun. ℹ It must be numeric or character. Backtrace:

1. scCNAutils::auto_cna_signal(...)
2. dplyr:::ungroup.grouped_df(., .data)
3. tidyselect::vars_select(names(x), ...)
   10. tidyselect:::eval_select_impl(...)
   11. tidyselect:::vars_select_eval(...)
   12. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   13. tidyselect:::eval_c(expr, data_mask, context_mask)
   14. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   15. tidyselect:::walk_data_tree(new, data_mask, context_mask)
   16. tidyselect:::as_indices_sel_impl(...)
   17. tidyselect:::as_indices_impl(x, vars, strict = strict)
   18. vctrs::vec_as_subscript(x, logical = "error")

R version executed: 4.1, ubuntu bionic 18.04.

[jmonlong]

I tried @andynkili fix on @PiStefania data, and it looks like it works now. Thanks @andynkili!