Error: Can't subset columns that don't exist. x Column `PEP` doesn't exist.

Question

[yueli7]

Hello,

I worked on R environment of parsemsf package. I have no idea of this error.

Thank you in advance for your great help!

Best,

Yue

>library(parsemsf)

>area_table <- make_area_table("LD-CS-150113_OstromR_OR_AC2_enriched.msf")
Error: Can't subset columns that don't exist.

x Column `PEP` doesn't exist.

Run `rlang::last_error()` to see where the error occurred.
In addition: Warning messages:
1: `chr_along()` is deprecated as of rlang 0.2.0.
This warning is displayed once per session. 
2: `new_overscope()` is deprecated as of rlang 0.2.0.
Please use `new_data_mask()` instead.
This warning is displayed once per session. 
3: `overscope_eval_next()` is deprecated as of rlang 0.2.0.
Please use `eval_tidy()` with a data mask instead.
This warning is displayed once per session. 
4: `overscope_clean()` is deprecated as of rlang 0.2.0.
This warning is displayed once per session. 


> rlang::last_error()
<error/vctrs_error_subscript_oob>
Can't subset columns that don't exist.
x Column `PEP` doesn't exist.
Backtrace:
1. parsemsf::quantitate(...)
4. parsemsf::make_area_table(reps[[i]])
5. parsemsf::make_pep_table(msf_file, min_conf, prot_regex, collapse)
7. dplyr:::select_.grouped_df(...)
8. dplyr:::select.grouped_df(.data, !!!dots)
9. dplyr:::.select_grouped_df(.data, !!!enquos(...), notify = TRUE)
10. tidyselect::vars_select(tbl_vars(.data), !!!enquos(...))
11. tidyselect:::eval_select_impl(...)
19. tidyselect:::vars_select_eval(...)
20. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
21. tidyselect:::eval_c(expr, data_mask, context_mask)
22. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
23. tidyselect:::walk_data_tree(new, data_mask, context_mask)
24. tidyselect:::as_indices_sel_impl(...)
25. tidyselect:::as_indices_impl(x, vars, strict = strict)
26. tidyselect:::chr_as_locations(x, vars)
27. vctrs::vec_as_location(x, n = length(vars), names = vars)
29. vctrs:::stop_subscript_oob(...)
30. vctrs:::stop_subscript(...)
Run `rlang::last_trace()` to see the full context.


> rlang::last_trace()
<error/vctrs_error_subscript_oob>
Can't subset columns that don't exist.
x Column `PEP` doesn't exist.
Backtrace:
     █
  1. ├─parsemsf::quantitate(...)
  2. │ ├─`%>%`(...)
  3. │ └─parsemsf::make_area_table(reps[[i]])
  4. │   └─parsemsf::make_pep_table(msf_file, min_conf, prot_regex, collapse)
  5. │     ├─dplyr::select_(pep_table, .dots = setNames(old_names, new_names))
  6. │     └─dplyr:::select_.grouped_df(...)
  7. │       └─dplyr:::select.grouped_df(.data, !!!dots)
  8. │         └─dplyr:::.select_grouped_df(.data, !!!enquos(...), notify = TRUE)
  9. │           └─tidyselect::vars_select(tbl_vars(.data), !!!enquos(...))
 10. │             └─tidyselect:::eval_select_impl(...)
 11. │               ├─tidyselect:::with_subscript_errors(...)
 12. │               │ ├─base::tryCatch(...)
 13. │               │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
 14. │               │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15. │               │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
 16. │               │ └─tidyselect:::instrument_base_errors(expr)
 17. │               │   └─base::withCallingHandlers(...)
 18. │               └─tidyselect:::vars_select_eval(...)
 19. │                 └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 20. │                   └─tidyselect:::eval_c(expr, data_mask, context_mask)
 21. │                     └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 22. │                       └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 23. │                         └─tidyselect:::as_indices_sel_impl(...)
 24. │                           └─tidyselect:::as_indices_impl(x, vars, strict = strict)
 25. │                             └─tidyselect:::chr_as_locations(x, vars)
 26. │                               └─vctrs::vec_as_location(x, n = length(vars), names = vars)
 27. │                                 └─(function () ...
 28. │                                   └─vctrs:::stop_subscript_oob(...)
 29. │                                     └─vctrs:::stop_subscript(...)
 30. └─dplyr::mutate_(., .dots = setNames(list(i), c("tech_rep")))

[brunobsouzaa]

Please, avoid posting it on two different sites. Either choose the most appropriate, here or stackoverflow.

Also, what have you already tried? Can you show some data? The error is pretty clear!

[yueli7]

@brunobsouzaa

Hello brunobsouzaa,

Thank you so much for your comments!

I think the error is the x Column PEP doesn't exist. Is that correct?

It is very strange to me that it works well on demo data, but not work well on my own data.

Thank you in advance for your great help!

Best,

Yue

[brunobsouzaa]

That's correct. It's pointing to a column that doesn't exists in your file!

[GenoMax]

yueli7 : Please do not accept comments/answers that do not address your problem as posted in the original solution.