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

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

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.

Author(s)

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/msQC documentation built on Oct. 31, 2024, 2:41 a.m.