rtAcquisitionRange: Retention time acquisition range (QC:4000139)

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

Retention time acquisition range (QC:4000139)

Description

"Upper and lower limit of time at which spectra are recorded." [PSI:QC] id: QC:4000139

#' 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 'spectra' 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

is_a: QC:4000004 ! n-tuple

Value

'numeric(2)'

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

tnaake/msQC documentation built on March 1, 2023, 8:11 p.m.