comp_report finds errors to be fixed in GAMBLR.data and GAMBLR.results

[vladimirsouza]

This bug happens when GAMBLR.data is loaded.

library(GAMBLR.datra)
> comp_report(this_sample = "HTMCP-01-06-00422-01A-01D",
+                   out = "reports/",
+                   export_individual_plots = TRUE)
Using the bundled CN segments (.seg) calls in GAMBLR.data...
Error:  You have given one or more unsupported or deprecated argument to  assign_cn_to_ssm . Please check the documentation and spelling of your arguments.
Offending argument(s): from_flatfile,use_augmented_maf

[vladimirsouza]

There is another error when GAMBLR.results is loaded.

>       comp_report(this_sample = "HTMCP-01-06-00422-01A-01D",
+                    out = "reports/",
+                    export_individual_plots = TRUE)
                                                                                                                   
Error in get_sample_wildcards(this_sample_id, seq_type) :                                                          
  object 'seq_type' not found
In addition: Warning message:
In if (tissue_status_filter == "normal") { :
  the condition has length > 1 and only the first element will be used

[mattssca]

Thanks for reporting this. I can have a look at this and propose a fix.