rtAcquisitionRange: Retention time acquisition range (QC:4000139)

View source: R/function_Spectra_metrics.R

rtAcquisitionRangeR Documentation

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, thomasnaake@googlemail.com

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/MsQuality documentation built on Dec. 1, 2022, 10:01 p.m.