Skip to contents

RSD filter

Source: R/rsd_filter.R
rsd_filter.Rd

An RSD filter calculates the relative standard deviation (the ratio of the standard deviation to the mean) for all features. Any feature with an RSD greater than a predefined threshold is excluded.

Usage

rsd_filter(rsd_threshold = 20, qc_label = "QC", factor_name, ...)

Arguments

rsd_threshold

(numeric) The RSD threshold above 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 rsd_filter object with the following output slots:

filtered(DatasetExperiment) A DatasetExperiment object containing the filtered data.
flags(data.frame) RSD and a flag indicating whether the feature was rejected by the filter or not.
rsd_qc(data.frame) The calculated RSD of the QC class.

Details

This object makes use of functionality from the following packages:

  • pmp

Inheritance

A rsd_filter object inherits the following struct classes:

[rsd_filter] >> [model] >> [struct_class]

References

Jankevics A, Lloyd GR, Weber RJM (2025). pmp: Peak Matrix Processing and signal batch correction for metabolomics datasets. doi:10.18129/B9.bioc.pmp https://doi.org/10.18129/B9.bioc.pmp, R package version 1.22.1, https://bioconductor.org/packages/pmp.

Examples

M = rsd_filter(
      rsd_threshold = 20,
      qc_label = "QC",
      factor_name = "V1")

M = rsd_filter(factor_name='Class')