# areaUnderTicRtQuantiles: area under TIC RT quantiles (MS:4000156) In tnaake/MsQuality: MsQuality - Quality metric calculation from Spectra and MsExperiment objects

 areaUnderTicRtQuantiles R Documentation

## area under TIC RT quantiles (MS:4000156)

### Description

MS:4000156
"The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple." [PSI:MS]

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%, 25%, 50%, 75%, and 100% quantiles of the retention time values are obtained,
(4) the ion count of the intervals between the 0%/25%, 25%/50%, 50%/75%, and 75%/100% are obtained,
(5) the ion counts of the intervals are summed (TIC) and the values returned.

### Usage

``````areaUnderTicRtQuantiles(spectra, msLevel = 1L, ...)
``````

### Arguments

 `spectra` `Spectra` object `msLevel` `integer` `...` not used here

### Details

MS:4000156
is_a: MS:4000004 ! n-tuple
is_a: MS:4000009 ! ID free
is_a: MS:4000017 ! chromatogram metric

The sum of the TIC is returned as an equivalent to the area.

### Value

`.numeric(4)`

### Note

This function interprets the *quantiles* from the [PSI:MS] definition as *quartiles*, i.e. the 0, 25, 50, 75 and 100% quantiles are used.

Thomas Naake

### 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)
areaUnderTicRtQuantiles(spectra = sps, msLevel = 2L)
``````

tnaake/MsQuality documentation built on Feb. 25, 2024, 7:32 p.m.