UpdateMummichogParameters

Input the name of the created mSetObj (see InitDataObjects).

mSetObj

Define the mass-spec instrument used to perform untargeted metabolomics.

instrumentOpt

Define the mass-spec mode of the instrument used to perform untargeted metabolomics.

msModeOpt

Numeric, specify the p-value cutoff to define significant m/z features from reference m/z features.

pvalCutoff

Logical, select adducts for mummichog to consider.

custom

This functions handles updating the mSet object for mummichog analysis. It is necessary to utilize this function
to specify to the organism's pathways to use (libOpt), the mass-spec mode (msModeOpt), mass-spec instrument (instrumentOpt), 
the p-value cutoff (pvalCutoff), and the number of permutations (permNum).

This package contains the R functions and libraries underlying the popular MetaboAnalyst web server, including 500 functions for data processing, normalization, statistical analysis, metabolite set enrichment analysis, metabolic pathway analysis, and biomarker analysis. The package is synchronized with the web server. After installing and loading the package, users will be able to reproduce the same results from their local computers using the corresponding R command history downloaded from MetaboAnalyst, to achieve maximum flexibility and reproducibility.

UpdateMummichogParameters: Update the mSetObj with user-selected parameters for MS Peaks to Pathways.

Description

Usage

Arguments