precursorIntensityMean: Precursor intensity distribution mean (QC:4000168),...

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

Precursor intensity distribution mean (QC:4000168), Identified precursor intensity distribution mean (QC:4000229), or Unidentified precursor intensity distribution mean (QC:4000234)

Description

"From the distribution of precursor intensities, the mean." [PSI:QC] id: QC:4000168

"From the distribution of identified precursor intensities, the mean" [PSI:QC] id: QC:4000229

"From the distribution of unidentified precursor intensities, the mean" [PSI:QC] id: QC:4000234

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 mean of the precursor intensity values is obtained ('NA' values are removed) and returned.

Usage

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

Arguments

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

Details

is_a: QC:4000003 ! single value is_a: QC:4000010 ! ID free is_a: QC:4000001 ! QC metric

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

The intensity distribution of the identified precursors informs about the dynamic range of the acquisition in relation to identifiability.

The intensity distribution of the unidentified precursors informs about the dynamic range of the acquisition in relation to identifiability.

Value

'numeric(1)'

Note

The 'Spectra' object might contain features that were (not) identified. If the calculation needs to be done according to *QC:4000229*/*QC:4000234*, the 'Spectra' object should be prepared accordingly.

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

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