readMZ: Read mzXML files

In Yang0014/MassSpectrometry: Tools for Glyco Native Mass Spectrometry Analysis

Description

Read mzXML files.

Usage

readMZ(fns, scanCounts = NULL, starts = NULL, ends = NULL)

Arguments

fns	character(n): the filenames of mzXML files.
scanCounts	integer(n): the scanCount to use in each file. If NULL, the last scan will be used.
starts	numeric(n): the start coordinates of the ranges.
ends	numeric(n): the end coordinates of the ranges.

Details

The peak intensities are normalised to the maximal intensity of 100 within eahc file.

Value

When starts and ends are NULL, a list of matrix with intensities will be returned. When they are given, a data.frame of the added intensities within the ranges will be returned.

Author(s)

Yang Yang

Examples

  mzFns <- system.file(c("threonine/threonine_i2_e35_pH_tree.mzXML",
                         "lockmass/LockMass_test.mzXML"),
                       package = "msdata")

  ## Read all the mzXML data
  allIntensities <- readMZ(mzFns)

  ## Read the peaks data within certain ragnges
  starts <- c(50, 70, 80)
  ends <- c(55, 75, 85)
  rangedIntensities <- readMZ(mzFns, starts=starts, ends=ends)

Yang0014/MassSpectrometry documentation built on May 10, 2019, 12:05 a.m.