Pandas version of as_matrix is deprecated

[RRCinci-Lu]

I was trying to use pandas version 1.0.0 with grnboost2. However, I ran into a problem where the as_matrix call part of grnboost2 does not work because it is deprecated (I think people use .values instead). Do you know a way to use the older version of pandas so I do not run into this problem?

Thanks, I am somewhat new to programming.

[rcannood]

You can try to pass your object as a matrix rather than a data frame.

Alternatively, you can force an older version of pandas with pip install --user "pandas<1.0"

[diegoalexespi]

I've been able to get around this by locally going into algo.py and changing line 214 from expression_matrix = expression_data.as_matrix() to expression_matrix = eexpression_data.as_numpy()

[deto]

@d93espinoza did you mean to_numpy instead of as_numpy?

[f6v]

The way to run it is:

network = grnboost2(expression_data=ex_matrix.to_numpy(), tf_names=tf_names, gene_names=ex_matrix.columns)

gene_names is required in case you pass a matrix as the input to the function.