tidyms.filter.DRatioFilter

class DRatioFilter(lb=0, ub=0.5, robust=False, verbose=False)

Remove Features with low biological information.

To use this filter the qc sample type and the study sample type must been specified in the DataContainer mapping.

Parameters:

lb: number between 0 and 1

Lower bound of acceptance

ub: number between 0 and 1

Upper bound of acceptance.

robust: bool

If True uses the MAD to compute the d-ratio. Else uses the standard deviation.

verbosebool

Shows a message with information after the correction has been applied.

Notes

D-Ratio is a metric defined in [1] as the quotient between the technical and the biological variation of a feature:

\[D-Ratio = \frac{\sigma_{technical}} {\sqrt{\sigma_{technical}^{2} + \sigma_{biological}^{2}}}\]

The technical variation is estimated as the dispersion from the QC samples, while the total variation (technical and biological) is estimated from the study samples. Lower D-Ratio values suggest features that are measured in a robust way. A maximum acceptance value of 0.5 is suggested.

References

[1]

D.Broadhurst et al, “Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies”, Metabolomics (2018) 14:72.

Constructor of the DRatioFilter.