dratio_filter: Dispersion ratio filter

In computational-metabolomics/structToolbox: Data processing & analysis tools for Metabolomics and other omics

Dispersion ratio filter

Description

The dispersion ratio (d-ratio) compares the standard deviation (or non-parametric equivalent) of the Quality Control (QC) samples relative to the standard deviation (or non-parametric equivalent) of the samples for each feature. If the d-ratio is greater than a predefined threshold then the observed sample variance could be due to technical variance and the feature is removed.

Usage

dratio_filter(threshold = 20, qc_label = "QC", factor_name, ...)

Arguments

threshold	(numeric) The threshold below which features are removed. The default is 20.
qc_label	(character) The label used to identify QC samples. The default is "QC".
factor_name	(character) The name of a sample-meta column to use.
...	Additional slots and values passed to struct_class.

Value

A dratio_filter object with the following output slots:

filtered	(DatasetExperiment) A DatasetExperiment object containing the filtered data.
flags	(data.frame) Flag indicating whether the feature was rejected by the filter or not.
d_ratio	(data.frame)

References

Broadhurst D, Goodacre R, Reinke SN, Kuligowski J, Wilson ID, Lewis MR, Dunn WB (2018). “Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies.” Metabolomics, 14(6).

Examples

D = MTBLS79_DatasetExperiment()
M = dratio_filter(threshold=20,qc_label='QC',factor_name='Class')
M = model_apply(M,D)

computational-metabolomics/structToolbox documentation built on Feb. 6, 2023, 2:43 p.m.