read.mzData: read.mzData.

In CorrectOverloadedPeaks: Correct Overloaded Peaks from GC-APCI-MS Data

read.mzData.

Description

read.mzData will import mzData as xcmsRaw-class objects.

Usage

read.mzData(filename, fmt = c("xcmsRaw", "xcmsRawLike"), verbose = FALSE)

Arguments

filename	A path to a mzData file (as exported by 'xcms::write.mzdata()').
fmt	Output format. Currently 'xcmsRaw' and 'xcmsRawLike' are supported. The latter is an S4 class similar to xcmsRaw but allowing to omit the xcms package.
verbose	Print messages to console.

Details

The main task of read.mzData functions is to import mzData files to R. Currently 'xcmsRaw' is supported as an output format. I created this function for legacy reasons as the mzData import is no longer supported by 'mzR' and consequently 'xcms' since 09/2021. This is a quick and dirty implementation. It will work only for mslevel=1 and a fixed set of base64 encoding parameters (size = 4, endian = "big"). However, feel free to send me an e-mail if you are interested in using the function but cant get it working.

Value

A generic R object of class xcmsRaw.

Examples

## Not run: 
  data(mzXML_data)
  write.mzXML(mzXML = mzXML_data, filename = "test.mzXML")
  x <- xcms::xcmsRaw("test.mzXML",  profstep=0)
  xcms::write.mzdata(x, file="test.mzData")
  x2 <- read.mzData(filename = "test.mzData")
  identical(str(x), str(x2))
  identical(x@env$intensity, x2@env$intensity)
  identical(x@env$mz, x2@env$mz)
  identical(x@scanindex, x2@scanindex)
  file.remove(c('test.mzData', 'test.mzXML'))
  
  # check that objects are independent (not identical)
  identical(methods::new("xcmsRawLike"), methods::new("xcmsRawLike"))

## End(Not run) 

CorrectOverloadedPeaks documentation built on April 3, 2025, 9:31 p.m.