createMZML: Create an mzML file

In Roestlab/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

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)

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.