extentIdentifiedPrecursorIntensity: Extent of identified precursor intensity (QC:4000125)

Description Usage Arguments Details Value Note Author(s) Examples

View source: R/function_Spectra_metrics.R

Description

"Ratio of 95th over 5th percentile of precursor intensity for identified peptides" [PSI:QC] id: QC:4000125

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

(2) the intensities of the precursor ions are obtained,

(3) the 5 ('NA' values are removed),

(4) the ratio between the 95 and returned.

Usage

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

Arguments

spectra

'Spectra' object

msLevel

'integer'

...

not used here

Details

Can be used to approximate the dynamic range of signal is_a: QC:4000003 ! single value is_a: QC:4000009 ! ID based is_a: QC:4000001 ! QC metric

Precursor intensity values that are 'NA' are removed.

Value

'numeric(1)'

Note

The 'Spectra' object might contain features that were not identified. If the calculation needs to be done according to *QC:4000125*, the 'Spectra' object should be prepared accordingly, i.e. being subsetted to spectra with identification data.

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$precursorIntensity <- c(100, 100, 100)
sps <- Spectra(spd)
extentIdentifiedPrecursorIntensity(spectra = sps, msLevel = 2L)

tnaake/MsQuality documentation built on Jan. 14, 2022, 7:34 p.m.