rtAcquisitionRange: retention time acquisition range (MS:4000070)

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

retention time acquisition range (MS:4000070)

Description

MS:4000070
"Upper and lower limit of retention time at which spectra are recorded." [PSI:MS]

The metric is calculated as follows:
(1) the Spectra object is filtered according to the MS level,
(2) the retention time values of the features within the Spectra object are obtained,
(3) the minimum and maximum retention time values are obtained and returned.

Usage

rtAcquisitionRange(spectra, msLevel = 1L, ...)

Arguments

spectra	Spectra object
msLevel	integer
...	not used here

Details

MS:4000070
is_a: MS:4000004 ! n-tuple
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_units UO:0000010 ! second
relationship: has_value_concept STATO:0000035 ! range

Value

numeric(2)

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)
rtAcquisitionRange(spectra = sps, msLevel = 2L)

tnaake/msQC documentation built on Jan. 30, 2025, 5:25 a.m.