cvCalc: calculate the analytical coefficient of variation from a set...

In WMBEdmands/MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets.

Description

calculate the coefficient of variation (CV%) for all LC-MS features of peak table using a set of observations (e.g. pooled quality control samples). The CV% is calculated according to the following equation:

CV\% = (δ / μ) * 100

where δ is the standard deviation and μ is the mean

Usage

cvCalc(peakTable = NULL, qcNames = NULL, thresh = 30)

Arguments

peakTable	either a data.frame, full file path as a character string to a .csv file of a peak table in the form observation (samples) in columns and variables (Mass spectral signals) in rows. If argument is not supplied a GUI (tcltk) file selection window will open and a .csv file can be selected.
qcNames	character vector quality control/ analytical replicate names to identify appropriate observation (sample) columns in peak table. with to calculate the coefficient of variance (CV%).
thresh	numeric the minimum CV% to retain an LC-MS variable (default = 30 i.e. 30%).

Value

a data frame similar to peakTable with any rows (LC-MS features) removed which are above the maximum CV% threshold. In addition a new column is added 'coeffVar' which contains the CV% calculated for each variable.

WMBEdmands/MetMSLine documentation built on May 9, 2019, 10:03 p.m.