medianTicRtIqr: median of TIC values in the RT range in which the middle half...

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

median of TIC values in the RT range in which the middle half of quantification data points are identified (MS:4000158)

Description

MS:4000158
"Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]

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 the Spectra object),
(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,
  identificationLevel = c("all", "identified", "unidentified"),
  ...
)

Arguments

spectra	Spectra object
msLevel	integer
identificationLevel	character(1), one of "all", "identified", or "unidentified"
...	not used here

Details

MS:4000158
is_a: MS:4000001 ! QC metric
is_a: MS:4000003 ! single value
is_a: MS:4000008 ! ID based

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

An attribute containing the PSI:MS term will only be returned if identificationLevel is "identified".

Value

numeric(1)

Note

The Spectra object might contain features that were not identified. If the calculation needs to be done according to *MS:4000158*, the Spectra object should be prepared accordingly, i.e. being subsetted to spectra with identification data.

Author(s)

Thomas Naake

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/msQC documentation built on Feb. 25, 2024, 7:33 p.m.