CV_filter: Filter metabolic data by CV

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

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)

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