Read.MSspec

Input the name of the created mSetObj (see InitDataObjects)

mSetObj

the name of the folder containing the MS spectra

folderName

specify the method to use for profile generation, supports "bin", "binlin",
"binlinbase" and "intlin"

profmethod

specify the full width at half maximum of the matched filtration
gaussian model peak

fwhm

define the bandwidth (standard deviation of the smoothing kernel) to be used

This function handles reading in LC/GC-MS spectra files and fills in the dataSet object.
It uses functions from the XCMS package to perform peak detection and alignment (grouping).

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.

Read.MSspec: Read LC/GC-MS spectra (.netCDF, .mzXML, mzData)

Description

Usage

Arguments