precursorIntensityRange: Precursor intensity range (QC:4000144)

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

Precursor intensity range (QC:4000144)

Description

"Minimum and maximum precursor intensity recorded." [PSI:QC] id: QC:4000144

The metric is calculated as follows: (1) the 'Spectra' object is filtered according to the MS level,

(2) the intensity of the precursor ions within 'spectra' are obtained,

(3) the minimum and maximum precursor intensity values are obtained and returned.

Usage

precursorIntensityRange(spectra, msLevel = 1, ...)

Arguments

spectra	'Spectra' object
msLevel	'integer'
...	not used here

Details

is_a: QC:4000010 ! ID free is_a: QC:4000001 ! QC metric is_a: QC:4000004 ! n-tuple

The intensity range of the precursors informs about the dynamic range of the acquisition.

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$precursorIntensity <- c(100.0, 100.0, 100.0)
sps <- Spectra(spd)
precursorIntensityRange(spectra = sps, msLevel = 2L)

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