ImportRawMSDataList: 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 provide a matrix with meta information about file such that each file has the name, file path, group class and extension type. 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

ImportRawMSDataList(
  dataset.meta,
  format = "png",
  dpi = 72,
  width = 9,
  par.cores = TRUE,
  plot = TRUE,
  bpis_name = "BPIS_",
  tics_name = "TICS_"
)

Arguments

dataset.meta	Matrix, input the meta data for files 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.
bpis_name	Character, input the name of the BPIS image to create.
tics_name	Character, input the name of the TICS image to create.

Author(s)

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.