from openomics.database.base import Annotatable
from openomics.transcriptomics import Expression
__all__ = ['SomaticMutation', 'DNAMethylation', 'CopyNumberVariation']
class SingleNucleotideVariants(Expression, Annotatable):
def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index",
transform_fn=None, dropna=False, npartitions=None, cohort_name=None):
"""
Args:
data:
transpose:
gene_index:
usecols:
gene_level:
sample_level:
transform_fn:
dropna:
npartitions:
cohort_name:
"""
super().__init__(data=data, transpose=transpose, gene_index=gene_index,
usecols=usecols, gene_level=gene_level,
sample_level=sample_level, transform_fn=transform_fn,
dropna=dropna, npartitions=npartitions, cohort_name=cohort_name)
@classmethod
def name(cls):
return cls.__name__
[docs]class SomaticMutation(Expression, Annotatable):
def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index",
transform_fn=None, dropna=False, npartitions=None, cohort_name=None):
"""
Args:
data:
transpose:
gene_index:
usecols:
gene_level:
sample_level:
transform_fn:
dropna:
npartitions:
cohort_name:
"""
super().__init__(data=data, transpose=transpose, gene_index=gene_index, usecols=usecols,
gene_level=gene_level, sample_level=sample_level,
transform_fn=transform_fn, dropna=dropna, npartitions=npartitions,
cohort_name=cohort_name)
[docs] @classmethod
def name(cls):
return cls.__name__
[docs]class DNAMethylation(Expression, Annotatable):
def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index",
transform_fn=None, dropna=False, npartitions=None, cohort_name=None):
"""
Args:
data:
transpose:
gene_index:
usecols:
gene_level:
sample_level:
transform_fn:
dropna:
npartitions:
cohort_name:
"""
super().__init__(data=data, transpose=transpose, gene_index=gene_index, usecols=usecols,
gene_level=gene_level, sample_level=sample_level,
transform_fn=transform_fn, dropna=dropna, npartitions=npartitions,
cohort_name=cohort_name)
[docs] @classmethod
def name(cls):
return cls.__name__
[docs]class CopyNumberVariation(Expression, Annotatable):
def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index",
transform_fn=None, dropna=False, npartitions=None, cohort_name=None):
"""
Args:
data:
transpose:
gene_index:
usecols:
gene_level:
sample_level:
transform_fn:
dropna:
npartitions:
cohort_name:
"""
super().__init__(data=data, transpose=transpose, gene_index=gene_index,
usecols=usecols, gene_level=gene_level, sample_level=sample_level,
transform_fn=transform_fn, dropna=dropna, npartitions=npartitions,
cohort_name=cohort_name)
[docs] @classmethod
def name(cls):
return cls.__name__