dot-rtOrderSpectra: Order Spectra according to increasing retention time

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

Order Spectra according to increasing retention time

Description

The function .rtOrderSpectra orders the features in a Spectra object according to the (increasing) retention time values.

Usage

.rtOrderSpectra(spectra)

Arguments

spectra

Spectra object

Details

Internal function in quality metric functions.

Value

Spectra object with the features ordered according to the (increasing) retention time

Author(s)

Johannes Rainer

Examples

library(S4Vectors)
library(Spectra)

spd <- DataFrame(
    msLevel = c(2L, 2L, 2L),
    polarity = c(1L, 1L, 1L),
    id = c("HMDB0001847", "HMDB0000001", "HMDB0000001"),
    name = c("Caffeine", "1-Methylhistidine", "1-Methylhistidine"))
## Assign m/z and intensity values
spd$mz <- list(
    c(56.0494, 69.0447, 83.0603, 109.0395, 110.0712,
        111.0551, 123.0429, 138.0662, 195.0876),
    c(109.2, 124.2, 124.5, 170.16, 170.52),
    c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16))
spd$intensity <- list(
    c(0.459, 2.585, 2.446, 0.508, 8.968, 0.524, 0.974, 100.0, 40.994),
    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))
spd$rtime <- c(15.84, 9.44, 9.44)
sps <- Spectra(spd)
MsQuality:::.rtOrderSpectra(sps)

tnaake/msQC documentation built on Jan. 30, 2025, 5:25 a.m.