Closed mattssca closed 1 year ago
Please don't submit a PR until the problem is fully fixed. Use a draft PR instead if you want feedback on the partial fix. I also would like to see working examples that test both modes of from_cache in the PR.
I have now marked this PR as a draft, I will update and provide the information you requested once it's ready for review. Thanks!
This function has now been updated with appropriate file paths for reading and exporting cached results. The function has also been getting a facelift in terms of expanded in-line comments, parameter descriptions and extended examples.
When testing this function I was not allowed to write to file: Error: Cannot open file for writing
However, I tested this function with from_cached = FALSE
and write_to_file = FALSE
for both genome
and capture
with success. As such:
genome_collated = collate_results(seq_type_filter = "genome", from_cache = FALSE, write_to_file = FALSE)
capture_collated = collate_results(seq_type_filter = "capture", from_cache = FALSE, write_to_file = FALSE)
I also tested using these_samples_metadata
and join_with_full_metadata
:
fl_metadata = get_gambl_metadata(seq_type_filter = "genome") %>% dplyr::filter(pathology == "FL")
fl_collated = collate_results(seq_type_filter = "genome", join_with_full_metadata = TRUE, these_samples_metadata = fl_metadata, write_to_file = FALSE, from_cache = FALSE)
Lastly, I tested this function with using the sample_table parameter as well:
fl_samples = get_gambl_metadata(seq_type_filter = "genome") %>% dplyr::filter(pathology == "FL") %>% dplyr::select(sample_id, patient_id, biopsy_id)
fl_collated = collate_results(sample_table = fl_samples, seq_type_filter = "genome", from_cache = FALSE, write_to_file = FALSE)
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