rtIqrRate: rate of the interquartile RT period for identified...

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

rate of the interquartile RT period for identified quantification data points (MS:4000154)

Description

MS:4000154
"The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. Higher rates indicate efficient sampling and identification. 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 retention time values are obtained,
(3) the 25% and 75% quantiles are obtained from the retention time values (NA values are removed),
(4) the number of eluted features between this 25% and 75% quantile is calculated,
(5) the number of features is divided by the interquartile range of the retention time and returned.

Usage

rtIqrRate(
  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:4000154
is_a: MS:4000003 ! single value
is_a: MS:4000008 ! ID based
is_a: MS:4000017 ! chromatogram metric
relationship: has_units UO:0000106 ! hertz synonym: "C-2B" RELATED [PMID:19837981]

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

Value

numeric(2)

Note

The Spectra object might contain features that were not identified. If the calculation needs to be done according to *MS:4000154*, the Spectra object should be prepared accordingly, i.e. being subsetted to spectra with identification data.

The stored retention time information in spectra might have a different unit than seconds. .rtIqr will return the IQR based on the values stored in spectra and will not convert these values to seconds.

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)
rtIqrRate(spectra = sps, msLevel = 2L)

tnaake/msQC documentation built on Oct. 31, 2024, 2:41 a.m.