mv_feature_filter {structToolbox}R Documentation

Filter by fraction missing values

Description

Filters features where the percent number of missing values exceeds a predefined threshold.

Usage

mv_feature_filter(
  threshold = 20,
  qc_label = "QC",
  method = "QC",
  factor_name,
  ...
)

Arguments

threshold

(numeric) The threshold for excluding features. The default is 20.

qc_label

(character) The label used to identify QC samples. The default is "QC".

method

(character) Filtering method. Allowed values are limited to the following:

  • "within_all": The filter is applied within classes.

  • "within_one": The filter is applied within any one class.

  • "QC": The filter is applied within QC samples.

  • "across": The filter is applied across all 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:

Value

A mv_feature_filter object.

References

Jankevics A, Weber RJM (2020). pmp: Peak Matrix Processing and signal batch correction for metabolomics datasets. R package version 1.1.0.

Examples

D = iris_DatasetExperiment()
M = mv_feature_filter(factor_name='Species',qc_label='versicolor')
M = model_apply(M,D)

[Package structToolbox version 1.2.0 Index]