ImportRawMSData: Import raw MS data

In simscr/metaboanalyst: 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,
  format = "png",
  dpi = 72,
  width = 9,
  par.cores = TRUE,
  plot = TRUE,
  plot.opts = "default"
)

Arguments

foldername	Character, input the file path to the folder containing the raw MS spectra to be processed.
format	Character, input the format of the image to create.
dpi	Numeric, input the dpi of the image to create.
width	Numeric, input the width of the image to create.
par.cores	Logical, if true, the function will automatically set the number of parallel cores. If false, it will not.
plot	Logical, if true the function will create BPIS and TICS plots.
plot.opts	By default, it will create BPIS and TICS plots using up to 10 samples per group. Set to "all" to create plots using all samples, though this may cause memory issues.

Author(s)

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

simscr/metaboanalyst documentation built on Jan. 21, 2020, 12:13 a.m.