rtIQRrate: Peptide identification rate of the interquartile RT period...

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

Description

"The identification rate of peptides for the interquartile retention time period, in peptides per second." [PSI:QC] id: QC:4000073

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 ('NA' values are removed),

(4) the number of eluted features between this 25 calculated,

(5) the number of features is divided by the interquartile range of the retention time and returned.

Usage

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

Arguments

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

Details

Higher rates indicate efficient sampling and identification. is_a: QC:4000003 ! single value is_a: QC:4000009 ! ID based is_a: QC:4000022 ! chromatogram metric

Value

'numeric(2)'

Note

The 'Spectra' object might contain features that were not identified. If the calculation needs to be done according to *QC:4000073*, 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, [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)
rtIqrRate(spectra = sps, msLevel = 2L)

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