ClassicalAnnotation: Title ClassicalAnnotation

View source: R/ClassicalAnnotation.R

ClassicalAnnotationR Documentation

Title ClassicalAnnotation

Description

Title ClassicalAnnotation

Usage

ClassicalAnnotation(
  peakTable,
  mgfFilePath,
  database,
  ionMode,
  CE = "all",
  tRCalibration = F,
  is.tR.file = NA,
  MS1DeltaMZ,
  MS1DeltaTR,
  MS1MS2DeltaTR,
  MS1MS2DeltaMZ,
  MS2DeltaMZ,
  NeedCleanSpectra = T,
  MS2NoiseRemoval = 0.01,
  onlyKeepMax = T,
  minScore = 0.5,
  KeepNotMatched = T,
  cores = 1
)

Arguments

peakTable

Peak table containing m/z and tr.

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.

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.

NeedCleanSpectra

T

MS2NoiseRemoval

0.01

onlyKeepMax

T

minScore

0.5

KeepNotMatched

T

cores

The number of CPU cores when computing.

mgfFile

The MGF file containing MS/MS information.

Value

ClassicalAnnotationRes


zhengfj1994/MetEx documentation built on Nov. 19, 2023, 1:34 p.m.