View source: R/function_Spectra_metrics.R
precursorIntensityMean | R Documentation |
"From the distribution of precursor intensities, the mean." [PSI:QC] id: QC:4000168
"From the distribution of identified precursor intensities, the mean" [PSI:QC] id: QC:4000229
"From the distribution of unidentified precursor intensities, the mean" [PSI:QC] id: QC:4000234
The metric is calculated as follows: (1) the 'Spectra' object is filtered according to the MS level,
(2) the intensity of the precursor ions within 'spectra' are obtained,
(3) the mean of the precursor intensity values is obtained ('NA' values are removed) and returned.
precursorIntensityMean(spectra, msLevel = 1L, ...)
spectra |
'Spectra' object |
msLevel |
'integer' |
... |
not used here |
is_a: QC:4000003 ! single value is_a: QC:4000010 ! ID free is_a: QC:4000001 ! QC metric
The intensity distribution of the precursors informs about the dynamic range of the acquisition.
The intensity distribution of the identified precursors informs about the dynamic range of the acquisition in relation to identifiability.
The intensity distribution of the unidentified precursors informs about the dynamic range of the acquisition in relation to identifiability.
'numeric(1)'
The 'Spectra' object might contain features that were (not) identified. If the calculation needs to be done according to *QC:4000229*/*QC:4000234*, the 'Spectra' object should be prepared accordingly.
Thomas Naake, thomasnaake@googlemail.com
library(S4Vectors) library(Spectra) spd <- DataFrame( msLevel = c(2L, 2L, 2L), polarity = c(1L, 1L, 1L), id = c("HMDB0000001", "HMDB0000001", "HMDB0001847"), name = c("1-Methylhistidine", "1-Methylhistidine", "Caffeine")) ## Assign m/z and intensity values spd$mz <- list( c(109.2, 124.2, 124.5, 170.16, 170.52), c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16), c(56.0494, 69.0447, 83.0603, 109.0395, 110.0712, 111.0551, 123.0429, 138.0662, 195.0876)) spd$intensity <- list( c(3.407, 47.494, 3.094, 100.0, 13.240), c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643), c(0.459, 2.585, 2.446, 0.508, 8.968, 0.524, 0.974, 100.0, 40.994)) spd$precursorIntensity <- c(100.0, 100.0, 100.0) sps <- Spectra(spd) precursorIntensityMean(spectra = sps, msLevel = 2L)
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