meanCharge: Mean charge in identified spectra (QC:4000177) or mean...

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

Mean charge in identified spectra (QC:4000177) or mean precursor charge in all MS2 (QC:4000182)

Description

"Mean charge in identified spectra" [PSI:QC] id: QC:4000177

"Mean precursor charge in all MS2" [PSI:QC] id: QC:4000182

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

(2) the precursor charge is obtained,

(3) the mean of the precursor charge values is calculated and returned.

Usage

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

Arguments

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

Details

is_a: QC:4000003 ! single value is_a: QC:4000009 ! ID based is_a: QC:4000001 ! QC metric

Value

'numeric(1)'

Note

The 'Spectra' object might contain features that were not identified. If the calculation needs to be done according to *QC:4000177*, 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$precursorCharge <- c(1L, 1L, 1L)
sps <- Spectra(spd)
meanCharge(spectra = sps, msLevel = 2L)

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