Description Usage Arguments Value References Examples
View source: R/batchMS2Score.parallel.R
Title batchMS2Score.parallel
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | batchMS2Score.parallel(
ms1Info,
ms1DeltaMZ,
ms2DeltaMZ,
deltaTR,
mgfMatrix,
mgfData,
MS2.sn.threshold = 3,
MS2.noise.intensity = "minimum",
MS2.missing.value.padding = "minimal.value",
ms2Mode = "ida",
scoreMode = "average",
diaMethod = "NA",
cores = 4
)
|
ms1Info |
the result of extracResFliter |
ms1DeltaMZ |
the difference of m/z between ms1Info and mgf files |
ms2DeltaMZ |
the difference of m/z between mgf and database of MS2 |
deltaTR |
the difference of retention time between ms1Info and mgf |
mgfMatrix |
the mgf mateix that created by importMgf |
mgfData |
the mgf mateix that created by importMgf |
MS2.sn.threshold |
The S/N threshold of MS2. |
MS2.noise.intensity |
The intensity of noise of MS2 spectrum. |
MS2.missing.value.padding |
The MS2 missing value padding method, "half" or "minimal.value" |
ms2Mode |
MS2 acquisition mode, 'ida' or 'dia', the default value is 'ida' |
scoreMode |
The MS2 score mode, default is "average". |
diaMethod |
If MS2 acquisition mode is "dia", a file save dia method should be provided. |
cores |
The number of CPU cores when computing. |
ms2ScoreResult
Tsugawa, Hiroshi , et al. "MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis." Nature Methods 12.6(2015):523-526.
1 2 3 4 5 6 7 8 9 10 | load(system.file("extdata/testData", "ms1InfoTest.rda", package = "MetEx"))
load(system.file("extdata/testData", "mgfMatrixTest.rda", package = "MetEx"))
load(system.file("extdata/testData", "mgfDataTest.rda", package = "MetEx"))
ms2ScoreResult <- batchMS2Score.parallel(ms1Info = ms1InfoTest,
ms1DeltaMZ = 0.01,
ms2DeltaMZ = 0.02,
deltaTR = 15,
mgfMatrix = mgfMatrixTest,
mgfData = mgfDataTest,
cores = 1)
|
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