createMZML {DIAlignR} | R Documentation

## Create an mzML file

### Description

Writes an mzML file having chromatograms and their native IDs.

### Usage

    createMZML(ropenms, filename, XICs, transitionIDs)

### Arguments

`ropenms` | (pyopenms module) get this python module through get_ropenms().
`filename` | (string) name of the mzML file to be written. Extension should be .chrom.mzML.
`XICs` | (list of list of data-frames) list of extracted ion chromatograms of all precursors.
`transitionIDs` | (list of integer) length must be the same as of XICs.

### Value

(None)

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-06-06

### See Also

`get_ropenms, addXIC`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    filename <- paste0(dataPath, "/xics/hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML")
    data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR)
    XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]]
    nativeIds <- list(27706:27711)
    ## Not run:
    ropenms <- get_ropenms(condaEnv = "envName")
    createMZML(ropenms, "testfile.chrom.mzML", XICs, nativeIds)
    mzR::chromatogramHeader(mzR::openMSfile("testfile.chrom.mzML", backend = "pwiz"))
    file.remove("testfile.chrom.mzML")

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]