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

Description Usage Arguments Details Value Note Author(s) Examples

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

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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, thomasnaake@googlemail.com

Examples

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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.