medianTICRTIQR: Median of TIC values in the RT range in which the middle half...

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

Description

"Median of TIC values in the RT range in which half of peptides are identified (RT values of Q1 to Q3 of identifications)" [PSI:QC] id: QC:4000130

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

(2) the 'Spectra' object is ordered according to the retention time,

(3) the features between the 1st and 3rd quartile are obtained (half of the features that are present in 'spectra'),

(4) the ion count of the features within the 1st and 3rd quartile is obtained,

(5) the median value of the ion count is calculated ('NA' values are removed) and the median value is returned.

Usage

medianTicRtIqr(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

The function 'medianTicRtIqr' uses the function [ionCount()] as an equivalent to the TIC.

Value

'numeric(1)'

Note

The 'Spectra' object might contain features that were not identified. If the calculation needs to be done according to *QC:4000130*, the 'Spectra' object should be prepared accordingly, i.e. being subsetted to spectra with identification data.

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$rtime <- c(9.44, 9.44, 15.84)
sps <- Spectra(spd)
medianTicRtIqr(spectra = sps, msLevel = 2L)

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