numberSpectra: Number of MS1 or MS2 spectra (QC:4000059/QC:4000060)

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

Number of MS1 or MS2 spectra (QC:4000059/QC:4000060)

Description

"The number of MS1 events in the run." [PSI:QC] id: QC:4000059 "The number of MS2 events in the run." [PSI:QC] id: QC:4000060

For *QC:4000059*, 'msLevel' is set to 1. For *QC:4000060*, 'msLevel' is set to 2.

Usage

numberSpectra(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:4000023 ! MS1 metric

Value

'numeric(1)'

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))
sps <- Spectra(spd)
numberSpectra(spectra = sps, msLevel = 1L)
numberSpectra(spectra = sps, msLevel = 2L)

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