View source: R/ClassicalAnnotation.R
ClassicalAnnotation | R Documentation |
Title ClassicalAnnotation
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
)
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. |
ClassicalAnnotationRes
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