ImportRawMSData: Import raw MS data

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

Description

This function handles the reading in of raw MS data (.mzML, .CDF and .mzXML). Users must set their working directory to the folder containing their raw data, divided into two subfolders named their desired group labels. The function will output two chromatograms into the user's working directory, a base peak intensity chromatogram (BPIC) and a total ion chromatogram (TIC). Further, this function sets the number of cores to be used for parallel processing. It first determines the number of cores within a user's computer and then sets it that number/2.

Usage

ImportRawMSData(foldername, mode = "onDisk", ncores = 4, plotSettings)

Arguments

foldername	Character, input the file path to the folder containing the raw MS spectra to be processed.
mode	Character, the data input mode. Default is "onDisk" to avoid memory crash. "inMemory" will absorb data into the memory.
plotSettings	List, plotting parameters produced by SetPlotParam Function. "plot.opts" can be added through this function for samples numbers for plotting. Defalut is "default", "all" will apply all samples for plotting and may cause memory crash, especially for large sample dataset.

Author(s)

Zhiqiang Pang [e-mail], Jasmine Chong [e-mail], Mai Yamamoto [e-mail], and 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.