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Fixes #185 #186

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Fixes #185 #186

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feba281
Drop drugs (columns) where all IC50 matrix entries are NA in BaseMode…
howard-lightfoot Jan 6, 2022
c5baba4
Company data packages: drop drugs with all NA results following tissu…
howard-lightfoot Jan 6, 2022
8238d2f
Remove deleted code
howard-lightfoot Jan 6, 2022
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6 changes: 2 additions & 4 deletions gdsctools/gdsc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -460,11 +460,9 @@ def create_data_packages_for_companies(self, companies=None):
# again but to hold various information
an = ANOVA(self.ic50, gf_filename, drug_decode_company, verbose=False)

def drug_to_keep(drug):
to_keep = drug in drug_decode_company.df.index
return to_keep
to_remove = set(an.ic50.drugIds).difference(set(drug_decode_company.df.index.tolist()))

an.ic50.df = an.ic50.df[drug_decode_company.df.index]
an.ic50.drop_drugs(list(to_remove))

an.settings = ANOVASettings(**self.settings)

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13 changes: 13 additions & 0 deletions gdsctools/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,19 @@ def __init__(
self.features.cosmicIds = self.ic50.cosmicIds
# self.cosmicIds = self.ic50.cosmicIds

# Also drop drugs (columns) where all matrix entries are NA
drugs_to_drop = self.ic50.df.isna().all()
number_kept = len(drugs_to_drop[~drugs_to_drop].index.tolist())
drugs_to_drop = drugs_to_drop[drugs_to_drop].index.tolist()
if len(drugs_to_drop) > 0 and self.verbose:
print(
"INFO: "
+ "%s drugs in your IC50 matrix" % len(drugs_to_drop)
+ " have no data. They will be dropped."
+ " %s drugs now in ANOVA analysis." % number_kept
)
self.ic50.drop_drugs(drugs_to_drop)

#: an instance of :class:`~gdsctools.settings.ANOVASettings`
self.settings = ANOVASettings()

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