chromatographyDuration: chromatography duration (MS:4000053)

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

chromatography duration (MS:4000053)

Description

MS:4000053 "The retention time duration of the chromatography in seconds." [PSI:MS]

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

chromatographyDuration(spectra, ...)

Arguments

spectra	Spectra object
...	not used here

Details

MS:4000053 synonym: "RT-Duration" RELATED [PMID:24494671]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000016 ! retention time metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_value_concept NCIT:C25330 ! Duration
relationship: has_units UO:0000010 ! second

Retention time values that are NA are removed.

Value

numeric(1)

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)
chromatographyDuration(spectra = sps)

tnaake/msQC documentation built on Feb. 25, 2024, 7:33 p.m.