read.mzData {CorrectOverloadedPeaks}

read.mzData.

Description

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

Usage

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

Arguments

filename

A mzData file as exported by 'xcms::write.mzdata()'.

fmt

Output format. Currently only xcmsRaw is supported.

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'))

## End(Not run)