morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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id_ease returns non-existing sample IDs in `these_samples` object. #248

Closed mattssca closed 9 months ago

mattssca commented 1 year ago

If non-existing sample IDs are provided, the function warns the user that no such samples are not found in the metadata. The downside is that the functions still retain these sample IDs in the these_samples object in the return from this function. The function should throw a warning about missing samples, but they should also be removed from the returned object.

id_ease(these_samples_metadata=GAMBLR.data::sample_data$meta,
+         these_sample_ids = c("r2d2","c3P0","Luke","Reddy_3812T"))

id_ease: WARNING! The following sample IDs were not found in the metadata:
[1] "r2d2" "c3P0" "Luke"

$this_metadata
  patient_id   sample_id Tumor_Sample_Barcode Sex COO_consensus LymphGen genetic_subgroup EBV_status_inf      cohort pathology reference_PMID
1 Reddy_3812 Reddy_3812T          Reddy_3812T   M           GCB      ST2             <NA>           <NA> dlbcl_reddy     DLBCL       28985567

$these_samples
[1] "r2d2"        "c3P0"        "Luke"        "Reddy_3812T"
rdmorin commented 9 months ago

Can this be closed @mattssca ?

mattssca commented 9 months ago

Yes, I am closing this now.