SetupMSdataMatrix

Input the name of the created mSetObj (see InitDataObjects)

mSetObj

name of peak column to enter into the returned matrix, if intvalue = 'into', 
use integrated area of original (raw) peak intensities, 
if intvalue = 'intf', use integrated area of filtered peak intensities, 
if intvalue = 'intb', use baseline corrected integrated peak intensities,
if intvalue = 'maxo', use the maximum intensity of original (raw) peaks, 
or if intvalue = 'maxf' use the maximum intensity of filtered peaks

intvalue

This function sets up a MS spectra data matrix using the 'groupval' function
from XCMS. This generates a usable matrix of peak values for analysis where 
columns represent peak groups and rows represent samples. 
Collisions where more than one peak from a single sample are in the same group get resolved
utilizing "medret", which uses the peak closest to the median retention time.

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.

SetupMSdataMatrix: Create a MS spectra data matrix of peak values for each group

Description

Usage

Arguments