QC_CV {MWASTools} | R Documentation |
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.
QC_CV (metabo_SE, CV_th = 0.30, plot_hist = TRUE, hist_bw = 0.005, hist_col = "moccasin", size_lab = 12, size_axis = 12)
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. |
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.
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.
## 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")