blankSub: substract blanks (i.e. negative controls/ background) from...

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

Description

calculate either the mean or median fold change between samples and blanks for every LC-MS variable and retain only LC-MS features above the blank fold change cut-off.

Usage

blankSub(peakTable = NULL, blankNames = NULL, sampNames = NULL,
  method = "mean", thresh = 2)

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 file selection window will open and a .csv file can be selected.
blankNames	character vector of blank (i.e. negative control) names to identify appropriate observation (blank) columns.
sampNames	character vector of sample names to identify appropriate observation (sample) columns.
method	character either 'median' or 'mean' fold change calculation.
thresh	numeric sample:blank fold change cut-off. Any LC-MS features below this threshold will be removed. (default = 2).

Value

a data frame similar to peakTable with any rows (LC-MS features) removed which are below the minimum blank fold change threshold.

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