def betas_table_aggregator_linreg(data,
annotations,
attributes,
observables_list,
data_params=None,
method_params=None):
"""
Producing table with information about observable-specificity of target data type
and target observable for each CpG.
Columns:
* item: CpG id.
* aux: gene, on which CpG is mapped.
* area_intersection_rel: relative intersection area of polygons
which is equals area of polygon(s) intersection to area of polygons union ratio.
* slope_intersection_rel: relative intersection area of allowed regions for slopes of linear regression.
* max_abs_slope: maximal absolute slope between all provided subjects subsets
* ...
* z_value: number of standard deviations by which data point is above the mean value.
* The considered data point is the difference between two linear regressions slopes.
* abs_z_value: absolute z_value
* p_value: probability of rejecting the null hypothesis that the difference in slopes is zero.
* ...
For each subjects subset the next columns are added to the resulting table:
* R2_***: determination coefficient.
A statistical measure of how well the regression line approximates the data points.
* intercept_***: estimated value of the intercept of linear regression.
* slope_***: estimated value of the slope of linear regression.
* intercept_std_***: standard error of the estimate of the intercept of linear regression.
* slope_std_***: standard error of the estimate of the slope of linear regression.
* intercept_p_value_***: p-value for the intercept of linear regression.
* slope_p_pvalue_***: p-value for the slope of linear regression.
* ...
Where *** is the name of subjects subset.
Possible parameters of experiment:
* None
:param data: pdm.Data instance, which specifies information about dataset.
:param annotations: pdm.Annotations instance, which specifies subset of CpGs.
:param attributes: pdm.Attributes instance, which specifies information about subjects.
:param observables_list: list of subjects subsets. Each element in list is dict,
where ``key`` is observable name and ``value`` is possible values for this observable.
:param method_params: parameters of experiment.
"""
table_aggregator_linreg(
DataType.betas,
data,
annotations,
attributes,
observables_list,
data_params,
method_params,
)
def entropy_table_aggregator_linreg(data,
annotations,
attributes,
observables_list,
data_params=None,
method_params=None):
table_aggregator_linreg(
DataType.entropy,
data,
annotations,
attributes,
observables_list,
data_params,
method_params,
)
def betas_adj_table_aggregator_linreg(
data,
annotations,
attributes,
observables_list,
data_params,
):
table_aggregator_linreg(
DataType.betas_adj,
data,
annotations,
attributes,
observables_list,
data_params=data_params,
)
def residuals_table_aggregator_linreg(
data,
annotations,
attributes,
observables_list,
data_params,
):
table_aggregator_linreg(
DataType.residuals,
data,
annotations,
attributes,
observables_list,
data_params=data_params,
)