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morinlab / GAMBLR.results

A collection of functions to access results of the Genomic Analysis of Mature B-cell Lymphomas
MIT License
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Vsouza hotfixes #13

Closed vladimirsouza closed 10 months ago

vladimirsouza commented 10 months ago

get_sample_wildcards was internally using get_gambl_metadata with a multivalue tissue_status_filter = c("normal", "tumour"), which is an old setup not supported anymore. Checking get_sample_wildcards code, I understand that tissue_status_filter = "normal" is what the function needs. Please, someone confirm this. Other changes are only indexation.

Kdreval commented 10 months ago

It is easy to track what the function needs. What is the output of this function on current master?

vladimirsouza commented 10 months ago

In main:

> get_sample_wildcards(this_sample_id = "00-15201_tumorA",
+                           this_seq_type = "genome")
Error in get_gambl_metadata(seq_type_filter = this_seq_type, tissue_status_filter = c("normal",  :                 
  `tissue_status_filter` argument should be either "tumour" or "normal".