ticQuantileToQuantileLogRatio: MS1 quantile TIC change ratio to Quantile 1 (QC:4000057) or...

Description Usage Arguments Details Value Note Author(s) Examples

View source: R/function_Spectra_metrics.R

Description

"The log ratio for the second to n-th quantile of TIC changes over first quantile of TIC changes." [PSI:QC] id: QC:4000057

"The log ratio for the second to n-th quantile of TIC over the previous quantile of TIC. For the boundary elements min/max are used." [PSI:QC] id: QC:4000058

Usage

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ticQuantileToQuantileLogRatio(spectra, relativeTo = "Q1", msLevel = 1L, ...)

Arguments

spectra

'Spectra' object

relativeTo

'character(1)', one of '"Q1"' or '"previous"'

msLevel

'integer'

...

not used here

Details

is_a: QC:4000004 ! n-tuple is_a: QC:4000010 ! ID free is_a: QC:4000022 ! chromatogram metric is_a: QC:4000023 ! MS1 metric

*TIC changes* are interpreted as follows: (1) the cumulative sum (‘cumsum') of the 'spectra'’s TIC is calculated (with spectra ordered by retention time),

(2) quartiles are then calculated on these,

(3) for *QC:4000057* the log2 ratio between the 25, 50, 75 and 100 ratios between the 25/0, 50/25, 75/50 and 100/75

The 'log2' values are returned instead of the 'log' values.

Value

'numeric(1)'

Note

This function interprets the *quantiles* from the [PSI:QC] definition as *quartiles*, i.e. the 0, 25, 50, 75 and 100

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))
sps <- Spectra(spd)
ticQuantileToQuantileLogRatio(spectra = sps, relativeTo = "Q1",
    msLevel = 2L)
ticQuantileToQuantileLogRatio(spectra = sps, relativeTo = "previous",
    msLevel = 2L)

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