areaUnderTicRtQuantiles | R Documentation |
"The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple." [PSI:QC] id: QC:4000078
The metric is calculated as follows: (1) the 'Spectra' object is filtered according to the MS level,
(2) the 'Spectra' object is ordered according to the retention time,
(3) the 0 are obtained,
(4) the ion count of the intervals between the 0 75
(5) the ion counts of the intervals are summed (TIC) and the values returned
areaUnderTicRtQuantiles(spectra, msLevel = 1L, ...)
spectra |
'Spectra' object |
msLevel |
'integer' |
... |
not used here |
is_a: QC:4000004 ! n-tuple is_a: QC:4000010 ! ID free is_a: QC:4000022 ! chromatogram metric
The sum of the TIC is returned as an equivalent to the area.
'numeric(4)'
This function interprets the *quantiles* from the [PSI:QC] definition as *quartiles*, i.e. the 0, 25, 50, 75 and 100
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$rtime <- c(9.44, 9.44, 15.84) sps <- Spectra(spd) areaUnderTicRtQuantiles(spectra = sps, msLevel = 2L)
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