rsd_filter: RSD filter

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

RSD filter

Description

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.

Details

This object makes use of functionality from the following packages:

• pmp

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.

Inheritance

A rsd_filter object inherits the following struct classes:

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

References

Jankevics A, Lloyd GR, Weber RJM (2023). 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 1.14.0, https://bioconductor.org/packages/pmp.

Examples

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

M = rsd_filter(factor_name='Class')

computational-metabolomics/structToolbox documentation built on Feb. 12, 2024, 2:15 a.m.