numberEmptyScans: number of empty MS1 scans (MS:4000099), number of empty MS2...

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

number of empty MS1 scans (MS:4000099), number of empty MS2 scans (MS:4000100), or number of empty MS3 scans (MS:4000101)

Description

MS:4000099
"Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS]

MS:4000100
"Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS]

MS:4000101
"Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS]

The metric is calculated as follows:
(1) the Spectra object is filtered according to the MS level,
(2) the intensities per entry are obtained,
(3) the number of intensity entries that are NULL, NA, or that have a sum of 0 are obtained and returned.

Usage

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

Arguments

spectra	Spectra object
msLevel	integer
...	not used here

Details

MS:4000099
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:integer ! The allowed value-type for this CV term

MS:4000100
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000022 ! MS2 metric
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:integer ! The allowed value-type for this CV term

MS:4000101
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:integer ! The allowed value-type for this CV term

#' For *MS:4000099*, msLevel is set to 1. For *MS:4000100*, msLevel is set to 2. For *MS:4000101*, msLevel is set to 3.

An attribute containing the PSI:MS term will only be returned if msLevel is either 1, 2, or 3.

Value

numeric(1)

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)
numberEmptyScans(spectra = sps, msLevel = 1L)
numberEmptyScans(spectra = sps, msLevel = 2L)

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