README.md

In parasitetwin/ExpMetFilter: Removes unwanted exposure compounds and their metabolites from the dataset

ExpMetFilter

An R-package designed to remove the exposure compound, its' metabolites and other impurities from non-targeted data analysis of toxicological exposure studies. Useful for metabolomics multivariate analysis but could also be used purely for removing blank features not caught by other data processing methods.

Installation

install.packages("devtools")
library("devtools")
install_github("parasitetwin/ExpMetFilter")

Functionality of package

"ExpMetFilter" - A function containing 5 different filter options for non-targeted data as well as the possiblity of internal standard correction of evaporation. The user controls which filters they want to apply to their dataset through the meta-data in the input file which can be found in "Example files".

"GapFilter" - A function which utilizes "Gap Status", gathered by Compound Discoverer (Thermo, USA), to filter out features which are not found in a specific sample type (as specified by the user).

Example files

"InputFileDescription" - Files which in-depth explains how datasets should be structured in order to be utilized by the two functions of this package.

"ExpMetFilter-ExampleFile" - A file containing two datasets (Orbitrap data from both HILIC and C18 chromatography analysis) of non-exposed embryos which have both undergone "GapFilter" and batchCorr processing.

parasitetwin/ExpMetFilter documentation built on Nov. 4, 2019, 11:18 p.m.