mzR (version 2.6.2)

openMSfile: Create and check mzR objects from netCDF, mzXML, mzData or mzML files.

Description

The openMSfile constructor will create a new format-specifc mzR object, open 'filename' file and all header information is loaded as a Rcpp module and made accessible through the ramp or pwiz slot of the resulting object. The openIDfile constructor will create a new format-specifc mzR object, open 'filename' file and all information is loaded as a Rcpp module. The mzid format is supported throught pwiz backend. Only mzIdentML 1.1 is supported.

Usage

openMSfile(filename, backend=c("Ramp", "pwiz", "netCDF"), verbose = FALSE)
 initializeRamp(object)
 isInitialized(object)
 fileName(object, ...)
 
 openIDfile(filename, verbose = FALSE)

Arguments

filename

Path name of the netCDF, mzData, mzXML or mzML file to read/write.

backend

A character specifiying with backend API to use. Currently 'Ramp', 'netCDF' and 'pwiz' are available.

object

An instantiated mzR object.

verbose

Enable verbose output.

...

Additional arguments, currently ignored.

Examples

library(msdata)
 filepath <- system.file("microtofq", package = "msdata")
 file <- list.files(filepath, pattern="MM14.mzML",
                     full.names=TRUE, recursive = TRUE)
 mz <- openMSfile(file)
 fileName(mz)
 runInfo(mz)
 close(mz)

 ## to use another backend
    mz <- openMSfile(file, backend = "pwiz")
    mz
  
  file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
  mzid <- openIDfile(file)
  softwareInfo(mzid)
  enzymes(mzid)