CV_filter {MWASTools} | R Documentation

## Filter metabolic data by CV

### Description

This function allows filtering a matrix of metabolic variables based on the coefficient of variation (CV) of each variable across the quality control (QC) samples. See also function "QC_CV()".

### Usage

    CV_filter(metabo_SE, CV_metabo, CV_th = 0.30)

### Arguments

`metabo_SE` | SummarizedExperiment object. See "MWAS_SummarizedExperiment()".
`CV_metabo` | numeric vector containing the CVs of the metabolic variables. See function "QC_CV()".
`CV_th` | numeric value indicating the CV threshold. Only features with CV below CV_th will be retained in the matrix.

### Value

A SummarizedExperiment object containing the CV-filtered metabolic_data.

### References

Dumas ME, et al. (2006). Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study. Analytical Chemistry, 78, 2199-1208.

### Examples

    ## Load data
    data(metabo_SE)

    ## Calculate CVs
    CV_metabo  <-  QC_CV (metabo_SE)

    ## Filter metabolic_data by CV
    metabo_CVfiltered <- CV_filter(metabo_SE, CV_metabo, CV_th = 0.30)
    metabo_CVfiltered2 <- CV_filter(metabo_SE, CV_metabo, CV_th = 0.15)

[Package MWASTools version 1.12.0 Index]