medianCharge: Median charge in identified spectra (QC:4000178) or median...

View source: R/function_Spectra_metrics.R

medianChargeR Documentation

Median charge in identified spectra (QC:4000178) or median precursor charge in all MS2 (QC:4000183)

Description

"Median charge in identified spectra" [PSI:QC] id: QC:4000178

"Median precursor charge in all MS2" [PSI:QC] id: QC:4000183

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 median of the precursor charge values is calculated and returned.

Usage

medianCharge(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:4000178*, the 'Spectra' object should be prepared accordingly.

Author(s)

Thomas Naake, thomasnaake@googlemail.com

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)
spd$precursorCharge <- c(1L, 1L, 1L)
medianCharge(spectra = sps, msLevel = 2L)

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