createMZML | R Documentation |
Writes an mzML file having chromatograms and their native IDs.
createMZML(ropenms, filename, XICs, transitionIDs)
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. |
(None)
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL-3 Date: 2020-06-06
get_ropenms, addXIC
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)
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