batchMS2Score: Title batchMS2Score

In zhengfj1994/MeTEA: Targeted extraction from untargeted metabolomics dataset by using metabolomics database

Description

Title batchMS2Score

Usage

batchMS2Score(
  ms1Info,
  ms1DeltaMZ,
  ms2DeltaMZ,
  deltaTR,
  mgfMatrix,
  mgfData,
  MS2.sn.threshold = 3,
  MS2.noise.intensity = "minimum",
  MS2.missing.value.padding = "half",
  ms2Mode = "ida",
  scoreMode = "average",
  diaMethod = "NA"
)

Arguments

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 data that created by inportMgf
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, there are two selection for this parameter, 'ida' and 'dia'
scoreMode	MS2 score mode, 'obverse','reverse' and 'average'
diaMethod	if the MS2 acquisition mode is dia, a diaMethod is necessary. If is ida, diaMethod can be set as "NA"

Value

ms2ScoreResult

References

Tsugawa, Hiroshi , et al. "MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis." Nature Methods 12.6(2015):523-526.

Examples

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(ms1Info = ms1InfoTest,
                                ms1DeltaMZ = 0.01,
                                ms2DeltaMZ = 0.02,
                                deltaTR = 15,
                                mgfMatrix = mgfMatrixTest,
                                mgfData = mgfDataTest)

zhengfj1994/MeTEA documentation built on June 29, 2021, 5:21 a.m.