medianTICofRTRange: Median of TIC values in the shortest RT range in which half...

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

Description

"Median of TIC values in the shortest RT range in which half of the peptides are identified" [PSI:QC] id: QC:4000132

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 number of features in 'spectra' is obtained and the number for half of the features is calculated,

(4) iterate through the features (always by taking the neighbouring half of features) and calculate the retention time range of the set of features,

(5) retrieve the set of features with the minimum retention time range,

(6) calculate from the set of (5) the median TIC ('NA' values are removed) and return it.

Usage

medianTicOfRtRange(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 'medianTicOfRtRange' 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:4000132*, 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)
medianTicOfRtRange(spectra = sps, msLevel = 2L)

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