annotationFromPeakTable: Title annotationFromPeakTable

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

Description

Title annotationFromPeakTable

Usage

annotationFromPeakTable(
  peakTable,
  mgfFile,
  database,
  ionMode,
  CE = "all",
  tRCalibration = F,
  is.tR.file = NA,
  MS1DeltaMZ,
  MS1DeltaTR,
  MS2.sn.threshold = 3,
  MS2.noise.intensity = "minimum",
  MS2.missing.value.padding = "half",
  ms2Mode = "ida",
  diaMethod = "NA",
  MS1MS2DeltaTR,
  MS1MS2DeltaMZ,
  MS2DeltaMZ,
  scoreMode = "average"
)

Arguments

peakTable	Peak table containing m/z and tr.
mgfFile	The MGF file containing MS/MS information.
database	The database used for identification.
ionMode	Positive ion mode is 'P', negative ion mode is 'N'.
CE	Collision energy，default value is 'all'.
tRCalibration	T or F, T will do retention time calibration and F will not.
is.tR.file	The retention time of internal standards which saved in a xlsx file.
MS1DeltaMZ	Delta m/z of MS1.
MS1DeltaTR	Delta retention time.
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'
diaMethod	If MS2 acquisition mode is "dia", a file save dia method should be provided.
MS1MS2DeltaTR	Delta retention time between MS1 and MS2.
MS1MS2DeltaMZ	Delta m/z between MS1 and MS2.
MS2DeltaMZ	Delta m/z between experimental MS2 and reference MS2.
scoreMode	The MS2 score mode, default is "average".

Value

annotationFromPeakTableRes

Examples

annotationFromPeakTableRes <- annotationFromPeakTable(
    peakTable = system.file("extdata/peakTable","example.csv", package = "MetEx"),
    mgfFile = system.file("extdata/mgf","example.mgf", package = "MetEx"),
    database = system.file("extdata/database","example_database.xlsx", package = "MetEx"),
    ionMode = "P",
    MS1DeltaMZ = 0.01,
    MS1DeltaTR = 120,
    MS1MS2DeltaTR = 5,
    MS1MS2DeltaMZ = 0.01,
    MS2DeltaMZ = 0.02)

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