rtOverTICquantile: RT over TIC quantile (QC:4000054)

In tnaake/MsQuality: MsQuality - Quality metric calculation via Spectra and MsExperiment objects

Description

"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

Usage

rtOverTicQuantile(
  spectra,
  probs = seq(0, 1, 0.25),
  msLevel = 1L,
  relative = TRUE,
  ...
)

Arguments

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()].

Details

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

Value

'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.

Author(s)

Thomas Naake, [e-mail], Johannes Rainer

Examples

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)

tnaake/MsQuality documentation built on Jan. 14, 2022, 7:34 p.m.