mv_sample_filter: Missing value sample filter

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

Missing value sample filter

Description

Removes samples where the percent number of missing values exceeds a threshold.

Usage

mv_sample_filter(mv_threshold = 20, ...)

Arguments

mv_threshold	(numeric) The maximum percentage of features with missing values in a sample. The default is 20.
...	Additional slots and values passed to struct_class.

Details

This object makes use of functionality from the following packages:

• pmp

Value

A mv_sample_filter object with the following output slots:

filtered	(DatasetExperiment) A DatasetExperiment object containing the filtered data.
flags	(data.frame) A flag indicating whether the sample was rejected. 0 = rejected.
percent_missing	(data.frame) % missing values for each sample.

Inheritance

A mv_sample_filter object inherits the following struct classes:

⁠[mv_sample_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 = mv_sample_filter(
      mv_threshold = 20)

C = mv_sample_filter()

computational-metabolomics/structtoolbox documentation built on Feb. 9, 2024, 8:19 a.m.