I'm attempting to run rank_test() on subgroups in an AnnData object, by making use of test.partition(). There appears to be a syntax error, where in the rank_test method of a partition, it passes the datatype into test.rank_test (starting around Line 1729):
for i, idx in enumerate(self.partition_idx):
DETestsSingle.append(rank_test(
data=self.x[idx, :],
grouping=grouping,
gene_names=self.gene_names,
sample_description=self.sample_description.iloc[idx, :],
is_sig_zerovar=is_sig_zerovar,
dtype=dtype
))
However, in test.rank_test(), dtype is not an acceptable key word argument:
def rank_test(
data: Union[anndata.AnnData, Raw, np.ndarray, scipy.sparse.csr_matrix, glm.typing.InputDataBase],
grouping: Union[str, np.ndarray, list],
gene_names: Union[np.ndarray, list] = None,
sample_description: pd.DataFrame = None,
is_logged: bool = False,
is_sig_zerovar: bool = True
):
This results in the following error being thrown: "rank_test() got an unexpected keyword argument 'dtype'".
I'm attempting to run rank_test() on subgroups in an AnnData object, by making use of test.partition(). There appears to be a syntax error, where in the rank_test method of a partition, it passes the datatype into test.rank_test (starting around Line 1729):
for i, idx in enumerate(self.partition_idx): DETestsSingle.append(rank_test( data=self.x[idx, :], grouping=grouping, gene_names=self.gene_names, sample_description=self.sample_description.iloc[idx, :], is_sig_zerovar=is_sig_zerovar, dtype=dtype ))
However, in test.rank_test(), dtype is not an acceptable key word argument: def rank_test( data: Union[anndata.AnnData, Raw, np.ndarray, scipy.sparse.csr_matrix, glm.typing.InputDataBase], grouping: Union[str, np.ndarray, list], gene_names: Union[np.ndarray, list] = None, sample_description: pd.DataFrame = None, is_logged: bool = False, is_sig_zerovar: bool = True ):
This results in the following error being thrown: "rank_test() got an unexpected keyword argument 'dtype'".