areaUnderTICRTquantiles: Area under TIC RT quantiles (QC:4000078)

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

Description

"The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple." [PSI:QC] id: QC:4000078

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 are obtained,

(4) the ion count of the intervals between the 0 75

(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

is_a: QC:4000004 ! n-tuple is_a: QC:4000010 ! ID free is_a: QC:4000022 ! 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:QC] definition as *quartiles*, i.e. the 0, 25, 50, 75 and 100

Author(s)

Thomas Naake, [e-mail]

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 Jan. 14, 2022, 7:34 p.m.