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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!
The text was updated successfully, but these errors were encountered:
tdietl
changed the title
n_top_feature in calculate_hvf()
n_top_feature in highly_variable_methylation_feature()
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 inALLCools/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!
The text was updated successfully, but these errors were encountered: