QC_CV {MWASTools} | R Documentation

## Calculate coefficients of variation

### Description

This function calculates the coefficient of variation (CV) ( |sd/mean| ) of each metabolic feature across the quality control (QC) samples. The CV distribution is represented in a histogram. This function can be used to assess the reproducibility of individual metabolic features. Notice that CV = 0.30 and CV = 0.15 are the thresholds established by the FDA guidelines for biomarker discovery and quantification, respectively.

### Usage

    QC_CV (metabo_SE, CV_th = 0.30, plot_hist = TRUE, hist_bw = 0.005,
           hist_col = "moccasin", size_lab = 12, size_axis = 12)

### Arguments

`metabo_SE` | SummarizedExperiment object. See "MWAS_SummarizedExperiment()".
`CV_th` | numeric value indicating the CV threshold.
`plot_hist` | logical constant indicating whether a histogram showing CV distribution will be plotted.
`hist_bw` | numeric value indicating histogram bin width.
`hist_col` | character string indicating the color to be used to fill the histogram bars.
`size_lab` | numeric value indicating the font size of x- and y-axis titles.
`size_axis` | numeric value indicating the font size of x- and y-axis labels.

### Value

A numeric vector containing the CV of each metabolic feature and a histogram showing CV distribution. In the histogram, CVs above 1 are set to 1.

### 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
    metabo_CV <-  QC_CV (metabo_SE)
    metabo_CV2 <-  QC_CV (metabo_SE, hist_bw = 0.008, hist_col = "lightblue")

[Package MWASTools version 1.16.0 Index]