MetExAnnotation: Title Annotate metabolites by MetEx in one line.

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

Description

Title Annotate metabolites by MetEx in one line.

Usage

MetExAnnotation(
  dbFile,
  ionMode,
  CE = "all",
  tRCalibration = F,
  is.tR.file = NA,
  msRawData,
  MS1deltaMZ,
  MS1deltaTR,
  entroThre,
  intThre,
  classficationMethod = "NoSVM",
  mgfFile,
  MS2.sn.threshold = 3,
  MS2.noise.intensity = "minimum",
  MS2.missing.value.padding = "half",
  MS1MS2DeltaMZ,
  MS2DeltaMZ,
  MS1MS2DeltaTR,
  scoreMode = "average",
  MS2scoreFilter,
  cores = 1
)

Arguments

dbFile	The file path of database.
ionMode	The ion mode of experiment, "P" or "N".
CE	Collision energy, the default value is "all".
tRCalibration	Whether to perform retention time calibration.
is.tR.file	If retention time calibration is performed, the retention time of IS saved in xlsx should be imported.
msRawData	The file path of mzXML file.
MS1deltaMZ	Tolerance of MS1.
MS1deltaTR	Tolerance of retention time between experiment and database.
entroThre	The information entropy threshold.
intThre	The peak height threshold.
classficationMethod	The classficatioin method of true signals and noises, "NoSVM" or "SVM" is avilable and "NoSVM" is the default value.
mgfFile	The file path of mgfFile.
MS2.sn.threshold	The S/N threshold of MS2 spectrum.
MS2.noise.intensity	The intensity of noise of MS2 spectrum.
MS2.missing.value.padding	The missing value padding method of MS2.
MS1MS2DeltaMZ	The tolerance of MS between MS1 and MS2.
MS2DeltaMZ	The tolerance of MS between experiment MS2 and database MS2.
MS1MS2DeltaTR	The tolerance of retention time between MS1 and MS2.
scoreMode	The score mode of MS2, the default value is "average".
MS2scoreFilter	The threshold of MS2 score.
cores	The CPU cores used for parallel computation.

Value

MetExAnnotationRes

Examples

MetExAnnotationRes <- MetExAnnotation(dbFile = system.file("extdata/database","example_database.xlsx", package = "MetEx"),
                ionMode = "P",
                CE = "all",
                msRawData = system.file("extdata/mzXML","example.mzXML", package = "MetEx"),
                MS1deltaMZ = 0.01,
                MS1deltaTR = 60,
                entroThre = 2,
                intThre = 270,
                mgfFile = system.file("extdata/mgf","example.mgf", package = "MetEx"),
                MS1MS2DeltaMZ = 0.01,
                MS2DeltaMZ = 0.02,
                MS1MS2DeltaTR = 12,
                MS2scoreFilter = 0.6,
                parallel.Computing = TRUE)

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