rtOverMsQuarters | R Documentation |
"The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by RT-Duration." [PSI:QC] id: QC:4000055
"The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by RT-Duration." [PSI:QC] id: QC:4000056
The metric is calculated as follows: (1) the retention time duration of the whole 'Spectra' object is determined (taking into account all the MS levels),
(2) the 'Spectra' object is filtered according to the MS level and subsequently ordered according to the retention time
(3) the MS events are split into four (approximately) equal parts,
(4) the relative retention time is calculated (using the retention time duration from (1) and taking into account the minimum retention time),
(5) the relative retention time values associated to the MS event parts are returned.
rtOverMsQuarters(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:4000021 ! retention time metric is_a: QC:4000023 ! MS1 metric
'numeric(4)'
'rtDuration' considers the total runtime (including MS1 and MS2 scans).
Thomas Naake, thomasnaake@googlemail.com, Johannes Rainer
library(S4Vectors) library(Spectra) spd <- DataFrame( msLevel = c(2L, 2L, 2L, 2L), polarity = c(1L, 1L, 1L, 1L), id = c("HMDB0000001", "HMDB0000001", "HMDB0001847", "unknown"), name = c("1-Methylhistidine", "1-Methylhistidine", "Caffeine", "unknown")) ## Assign m/z and intensity values spd$mz <- list( c(109.2, 124.2, 124.5, 170.16, 170.52), c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16), c(56.0494, 69.0447, 83.0603, 109.0395, 110.0712, 111.0551, 123.0429, 138.0662, 195.0876), c(83.0603, 195.0876)) spd$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), c(3.146, 61.611)) spd$rtime <- c(9.44, 9.44, 15.84, 15.81) sps <- Spectra(spd) rtOverMsQuarters(spectra = sps, msLevel = 2L)
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