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

In xia-lab/MetaboAnalystR3.0: An R Package for Comprehensive Analysis of Metabolomics Data

Description

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.

Usage

SetupMSdataMatrix(mSetObj, intvalue)

Arguments

mSetObj

Input the name of the created mSetObj (see InitDataObjects)

intvalue

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

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR3.0 documentation built on May 6, 2020, 11:03 p.m.