precursorIntensitySD: Precursor intensity distribution sigma (QC:4000169),...

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

Precursor intensity distribution sigma (QC:4000169), Identified precursor intensity distribution sigma (QC:4000230), or Unidentified precursor intensity distribution sigma (QC:4000235)

Description

"From the distribution of precursor intensities, the sigma value." [PSI:QC] id: QC:4000169

"From the distribution of identified precursor intensities, the sigma value" [PSI:QC] id: QC:4000230

"From the distribution of unidentified precursor intensities, the sigma value" [PSI:QC] id: QC:4000235

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 standard deviation of precursor intensity values is obtained ('NA' values are removed) and returned.

Usage

precursorIntensitySd(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:4000230*/*QC:4000235*, 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)
precursorIntensitySd(spectra = sps, msLevel = 2L)

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