rtOverTicQuantile | R Documentation |
"The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of quantiles observed is given by the size of the tuple." [PSI:QC] id: QC:4000054
The metric is calculated as follows: (1) the 'Spectra' object is ordered according to the retention time,
(2) the cumulative sum of the ion count is calculated (TIC),
(3) the quantiles are calculated according to the 'probs' argument, e.g. when 'probs' is set to 'c(0, 0.25, 0.5, 0.75, 1)' the 0 100
(4) the retention time/relative retention time (retention time divided by the total run time taking into account the minimum retention time) is calculated,
(5) the (relative) duration of the LC run after which the cumulative
rtOverTicQuantile( spectra, probs = seq(0, 1, 0.25), msLevel = 1L, relative = TRUE, ... )
spectra |
'Spectra' object |
probs |
'numeric' defining the quantiles. See [stats::quantile()] for details. Defaults to 'probs = seq(0, 1, 0.25)'. |
msLevel |
'integer' |
relative |
'logical', if set to 'TRUE' the relative retention time will be returned instead of the abolute retention time |
... |
additional arguments passed to [stats::quantile()]. |
is_a: QC:4000004 ! n-tuple is_a: QC:4000010 ! ID free is_a: QC:4000021 ! retention time metric is_a: QC:4000022 ! chromatogram metric
'numeric' of length equal to length 'probs' with the relative duration (duration divided by the total run time) after which the TIC exceeds the respective quantile of the TIC.
Thomas Naake, thomasnaake@googlemail.com, Johannes Rainer
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) rtOverTicQuantile(spectra = sps, msLevel = 2L)
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