tidyms.filter.VariationFilter

class VariationFilter(lb=0, ub=0.25, process_classes=None, robust=False, intraclass=True, verbose=False)

Remove features with low reproducibility.

The reproducibility of the features is evaluated using the Relative standard deviation of each feature in samples of a specific class or classes. By default, the QC samples are analyzed.

Parameters:

lbnumber between 0 and 1

Lower bound of acceptance

ubnumber between 0 and 1

Upper bound of acceptance. Must be greater than lb.

process_classes: List[str], optional

Classes used to evaluate the coefficient of variation. If None, list of classes is taken from the qc sample type from the DataContainer mapping attribute.

robust: bool

If false uses the mean and standard deviation to compute the cv. Else, the cv is estimated using the MAD and the median of the feature, assuming a normal distribution.

intraclass: bool

If True, the cv is computed for each class in process_classes and then the maximum value is compared against lb and ub. Else a global cv is computed for all classes in process_classes.

verbose: bool

If True, prints a message

Constructor of the VariationFilter.