CV_filter {MWASTools} | R Documentation |
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()".
CV_filter(metabo_SE, CV_metabo, CV_th = 0.30)
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. |
A SummarizedExperiment object containing the CV-filtered metabolic_data.
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 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)