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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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Fix id_ease when metadata and seq_type are provided #55

Closed vladimirsouza closed 6 months ago

vladimirsouza commented 6 months ago

This is the .results version of the same fix in .data (this PR).

> my_meta = get_gambl_metadata() %>% 
+   filter(pathology %in% c("BL", "DLBCL", "FL"))

#### using verbose = FALSE
> meta2 = id_ease(these_samples_metadata = my_meta,
+                 these_sample_ids = NULL,
+                 verbose = FALSE,
+                 this_seq_type = "capture")
id_ease: WARNING! 1288 samples in the provided metadata were removed because their seq types are not the same as in the `set_type` argument. Use `verbose = TRUE` to see their IDs.

#### using verbose = TRUE
> meta2 = id_ease(these_samples_metadata = my_meta,
+                 these_sample_ids = NULL,
+                 verbose = TRUE,
+                 this_seq_type = "capture")
id_ease: Metadata is provided and samples of the selected seq type are kept...
id_ease: WARNING! 1288 samples in the provided metadata were removed because their seq types are not the same as in the `set_type` argument. Their first 100 IDs are:

# the first 100 sample ids are shown. 

id_ease: No sample IDs provided, all sample IDs in the metadata will be kept...
id_ease: Returning metadata for 0 samples...