rtDuration: RT duration (QC:4000053)

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

Description

"The retention time duration of the MS run in seconds, similar to the highest scan time minus the lowest scan time." [PSI:QC] id: QC:4000053

The metric is calculated as follows: (1) the retention time associated to the individual Spectra is obtained,

(2) the maximum and the minimum of the retention time is obtained,

(3) the difference between the maximum and the minimum is calculated and returned.

Usage

rtDuration(spectra, ...)

Arguments

spectra	'Spectra' object
...	not used here

Details

is_a: QC:4000003 ! single value is_a: QC:4000010 ! ID free is_a: QC:4000021 ! retention time metric

Retention time values that are 'NA' are removed.

Value

'numeric(1)'

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)
rtDuration(spectra = sps)

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