batchMS2Score.parallel: Title batchMS2Score.parallel

Description Usage Arguments Value References Examples

View source: R/batchMS2Score.parallel.R

Description

Title batchMS2Score.parallel

Usage

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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
)

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 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.

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

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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)

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