mv_feature_filter: Filter by fraction missing values

In structToolbox: Data processing & analysis tools for Metabolomics and other omics

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:

• pmp

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)

structToolbox documentation built on Nov. 8, 2020, 6:54 p.m.