View source: R/function_Spectra_metrics.R
rtDuration | R Documentation |
"The retention time duration of the MS run in seconds, similar to the highest scan time minus the lowest scan time." [PSI:QC] id: QC:4000053
The metric is calculated as follows: (1) the retention time associated to the individual Spectra is obtained,
(2) the maximum and the minimum of the retention time is obtained,
(3) the difference between the maximum and the minimum is calculated and returned.
rtDuration(spectra, ...)
spectra |
'Spectra' object |
... |
not used here |
is_a: QC:4000003 ! single value is_a: QC:4000010 ! ID free is_a: QC:4000021 ! retention time metric
Retention time values that are 'NA' are removed.
'numeric(1)'
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) rtDuration(spectra = sps)
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