process_monospectra: process_monospectra

In MGMS2: 'MGMS2' for Polymicrobial Samples

Description

This function processes multiple mzXML files which are listed in the file that an user specifies.

Usage

process_monospectra(
  file,
  mass.range = c(1000, 2200),
  halfWindowSize = 20,
  SNIP.iteration = 60
)

Arguments

file	A file name. This file is a tab-delimited file which contains the following columns: file names, strain.no, and strain. See below for details.
mass.range	The m/z range that users want to consider for the analysis. (Default: c(1000,2200)).
halfWindowSize	A half window size used for the smoothing the intensity values. (Default: 20). See smoothIntensity for details.
SNIP.iteration	An iteration used to remove the baseline of an spectrum. (Default: 60). See removeBaseline for details.

Value

A list of processed monobacterial mass spectra (S4 objects, MALDIquant MassSpectrum objects), and their strain numbers (a vector), unique strains (a vector), and strain names (a vector).

Examples

spectra.processed.A <- process_monospectra(
   file=system.file("extdata", "listA.txt", package="MGMS2"),
   mass.range=c(1000,2200))

MGMS2 documentation built on April 24, 2020, 9:06 a.m.