rtAcquisitionRange: Retention time acquisition range (QC:4000139)

Description Usage Arguments Details Value Author(s) Examples

View source: R/function_Spectra_metrics.R

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

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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

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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 Jan. 14, 2022, 7:34 p.m.