nimare.correct
.FDRCorrector
- class FDRCorrector(method='indep', alpha=0.05, **kwargs)[source]
Bases:
Corrector
Perform false discovery rate correction on a meta-analysis.
- Parameters:
Notes
This corrector supports a small number of internal FDR correction methods, but can also use special methods implemented within individual Estimators. To determine what methods are available for the Estimator you’re using, use
inspect()
. Estimators have special methods following the naming conventioncorrect_[correction-type]_[method]
(e.g.,correct_fdr_indep
).Methods
Perform Benjamini-Hochberg FDR correction.
Perform Benjamini-Yekutieli FDR correction.
get_params
([deep])Get parameters for this estimator.
inspect
(result)Identify valid 'method' values for a MetaResult object.
load
(filename[, compressed])Load a pickled class instance from file.
save
(filename[, compress])Pickle the class instance to the provided file.
set_params
(**params)Set the parameters of this estimator.
transform
(result)Apply the multiple comparisons correction method to a MetaResult object.
- correct_fdr_indep(p)[source]
Perform Benjamini-Hochberg FDR correction.
This correction is based on the one described in Benjamini and Hochberg[1]. This method is not universally appropriate. It works well for tests that are independent, or which are positively correlated.
Warning
Do not call this method directly. Call
transform()
withmethod='indep'
instead.New in version 0.0.12.
- Parameters:
p (
numpy.ndarray
) – A 1D array of p values.- Returns:
p_corr (
numpy.ndarray
) – A 1D array of adjusted p values.tables (
dict
) – A dictionary of DataFrames with summary information from the correction. This correction method does not produce any tables, so it will be an empty dict.description_ (
str
) – A description of the correction procedure.
References
See also
- correct_fdr_negcorr(p)[source]
Perform Benjamini-Yekutieli FDR correction.
This correction is based on the one described in Benjamini and Yekutieli[2]. It is most appropriate for tests that are negatively correlated.
Warning
Do not call this method directly. Call
transform()
withmethod='negcorr'
instead.New in version 0.0.12.
- Parameters:
p (
numpy.ndarray
) – A 1D array of p values.- Returns:
p_corr (
numpy.ndarray
) – A 1D array of adjusted p values.tables (
dict
) – A dictionary of DataFrames with summary information from the correction. This correction method does not produce any tables, so it will be an empty dict.description_ (
str
) – A description of the correction procedure.
Notes
The difference between the Benjamini-Yekutieli and Benjamini-Hochberg methods is that Benjamini-Yekutieli includes an additional term,
c(m)
. When the tests are independent or positively correlated,c(m)
is 1 (and thus has no effect). In cases of other forms of dependence,c(m)
has an effect.References
See also
- classmethod inspect(result)[source]
Identify valid ‘method’ values for a MetaResult object.
In addition to returning a list of valid values, this method will also print out those values, divided by the value type (Estimator or generic).
- Parameters:
result (
MetaResult
) – Object for which valid correction methods (i.e., ‘method’ values) will be identified.- Returns:
List of valid ‘method’ values for the Corrector+Estimator combination, including both non-specific methods and Estimator-specific ones.
- Return type:
- classmethod load(filename, compressed=True)[source]
Load a pickled class instance from file.
- Parameters:
- Returns:
obj – Loaded class object.
- Return type:
class object
- set_params(**params)[source]
Set the parameters of this estimator.
The method works on simple estimators as well as on nested objects (such as pipelines). The latter have parameters of the form
<component>__<parameter>
so that it’s possible to update each component of a nested object.- Return type:
self
- transform(result)[source]
Apply the multiple comparisons correction method to a MetaResult object.
- Parameters:
result (
MetaResult
) – MetaResult generated by an Estimator to be corrected for multiple comparisons.- Returns:
result – MetaResult with new corrected maps, tables, and description added.
- Return type: