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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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GAMBLR.results can't find `liftover_bedpe` function #49

Open vladimirsouza opened 7 months ago

vladimirsouza commented 7 months ago

When running devtools::check():

get_manta_sv_by_sample: no visible global function definition for
  ‘liftover_bedpe’

From get_manta_sv_by_sample's examples:

> my_sv = get_manta_sv_by_sample(this_sample_id = "99-27783_tumorA",
+                                these_samples_metadata = get_gambl_metadata(),
+                                projection = "hg38",
+                                force_lift = TRUE)
Reading 99-27783_tumorA from: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/manta_current/99-outputs/bedpe/genome--grch37/somaticSV/99-27783_tumorA--99-27783_normal--matched.somaticSV.bedpe
Error in liftover_bedpe(bedpe_df = bedpe_dat_raw, target_build = projection) :                                             
  could not find function "liftover_bedpe"