ticQuartileToQuartileLogRatio: MS1 TIC-change quartile ratios (MS:4000057) or MS1 TIC...

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

MS1 TIC-change quartile ratios (MS:4000057) or MS1 TIC quartile ratios (MS:4000058)

Description

MS:4000057
"The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3" [PSI:MS]
For calculation of MS:400057 set mode = "TIC_change".

MS:4000058
"The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3." [PSI:MS]
For calculation of MS:400058 set mode = "TIC".

The metric is calculated as follows:
(1) the TIC (ionCount) of the Spectra object is calculated per scan event (with spectra ordered by retention time),
(2) for *MS:4000057*, the differences between TIC values are calculated between subsequent scan events, for *MS:4000058*, the TIC values between subsequent scan events are taken as they are,
(3) for *MS:4000057* and *MS:4000058* the ratios between the 25%, 50%, 75%, and 100% quantile to the 25% quantile of the values of (2) are calculated. Alternatively, if relativeTo = "Q1", the ratios are calculated between the 50%/25%, 75%/25%, and 100%/25% quantiles,
(4) The log values of the ratios are returned.

Usage

ticQuartileToQuartileLogRatio(
  spectra,
  relativeTo = c("previous", "Q1"),
  mode = c("TIC_change", "TIC"),
  msLevel = 1L,
  ...
)

Arguments

spectra	Spectra object
relativeTo	character(1), one of "Q1" or "previous"
mode	character(1), one of "TIC_change" or "TIC"
msLevel	integer
...	not used here

Details

MS:4000057
synonym: "MS1-TIC-Change-Q2" RELATED [PMID:24494671]
synonym: "MS1-TIC-Change-Q3" RELATED [PMID:24494671]
synonym: "MS1-TIC-Change-Q4" RELATED [PMID:24494671]
is_a: MS:4000004 ! n-tuple
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000017 ! chromatogram metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_value_concept STATO:0000105 ! log signal intensity ratio

MS:4000058
synonym: "MS1-TIC-Q2" RELATED [PMID:24494671]
synonym: "MS1-TIC-Q3" RELATED [PMID:24494671]
synonym: "MS1-TIC-Q4" RELATED [PMID:24494671]
is_a: MS:4000004 ! n-tuple
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000017 ! chromatogram metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_value_concept STATO:0000105 ! log signal intensity ratio

An attribute containing the PSI:MS term will only be returned if relativeTo is "previous" and msLevel is 1.

Value

numeric(1)

Note

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

Author(s)

Thomas Naake

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))
sps <- Spectra(spd)

## MS:4000057
ticQuartileToQuartileLogRatio(spectra = sps, relativeTo = "previous",
    msLevel = 2L, mode = "TIC_change")
ticQuartileToQuartileLogRatio(spectra = sps, relativeTo = "Q1",
    msLevel = 2L, mode = "TIC_change")

## MS:4000058
ticQuartileToQuartileLogRatio(spectra = sps, relativeTo = "previous",
    msLevel = 2L, mode = "TIC")
ticQuartileToQuartileLogRatio(spectra = sps, relativeTo = "Q1",
    msLevel = 2L, mode = "TIC")

tnaake/msQC documentation built on Oct. 31, 2024, 2:41 a.m.