QC_CV: Calculate coefficients of variation

In MWASTools: MWASTools: an integrated pipeline to perform metabolome-wide association studies

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")

MWASTools documentation built on Nov. 8, 2020, 5:07 p.m.