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n_top_feature in highly_variable_methylation_feature() #54

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tdietl opened this issue Aug 9, 2024 · 0 comments
Open

n_top_feature in highly_variable_methylation_feature() #54

tdietl opened this issue Aug 9, 2024 · 0 comments

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@tdietl
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tdietl commented Aug 9, 2024

Dear team,

Thanks for developing this great tool!
I noticed a minor issue when using the function highly_variable_methylation_feature() as defined in ALLCools/mcds/utilities.py

n_top_feature is supposed to be a parameter that can be changed by the user. However, in this function in line 263 it is defined as 5000, see: feature_subset = df.index.isin(df.sort_values("dispersion_norm", ascending=False).index[:5000])

Therefore, I would propose to change it to:
feature_subset = df.index.isin(df.sort_values("dispersion_norm", ascending=False).index[:n_top_feature])

Thanks!

@tdietl tdietl changed the title n_top_feature in calculate_hvf() n_top_feature in highly_variable_methylation_feature() Aug 9, 2024
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