rtIQR: Interquartile RT period for peptide identifications...

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

Description

"The interquartile retention time period, in seconds, for all peptide identifications over the complete run." [PSI:QC] id: QC:4000072

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 interquartile range is obtained from the values and returned ('NA' values are removed).

Usage

rtIqr(spectra, msLevel = 1L, ...)

Arguments

spectra	'Spectra' object
msLevel	'integer'
...	not used here

Details

Longer times indicate better chromatographic separation. is_a: QC:4000003 ! single value is_a: QC:4000009 ! ID based is_a: QC:4000022 ! chromatogram metric

Retention time values that are 'NA' are removed.

Value

'numeric(1)'

Note

The 'Spectra' object might contain features that were not identified. If the calculation needs to be done according to *QC:4000072*, the 'Spectra' object should be prepared accordingly, i.e. 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, [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)
rtIqr(spectra = sps, msLevel = 2L)

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