openMSfile {mzR} | R Documentation

## 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 = NULL, 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(1)` specifiying which backend API to use. Currently 'Ramp', 'netCDF' and 'pwiz' are supported. If `backend = NULL` (the default), the function tries to determine the backend to be used based on either the file extension of the file content.
`object` | An instantiated mzR object.
`verbose` | Enable verbose output.
`...` | Additional arguments, currently ignored.

### Author(s)

Steffen Neumann, Laurent Gatto, Qiang Kou

### 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)

     ## Not run:
        ## to use another backend
        mz <- openMSfile(file, backend = "pwiz")
        mz

    ## End(Not run)

      file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
      mzid <- openIDfile(file)
      softwareInfo(mzid)
      enzymes(mzid)

[Package mzR version 2.16.2 Index]