calculateMetricsFromMsExperiment: Calculate QC metrics from a MsExperiment object

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

Calculate QC metrics from a MsExperiment object

Description

The function calculateMetricsFromMsExperiment calculates quality metrics from a MsExperiment object. Each spectra in the msexp object should refer to one mzML file/to one sample.

Usage

calculateMetricsFromMsExperiment(
  msexp,
  metrics = qualityMetrics(msexp),
  filterEmptySpectra = FALSE,
  ...,
  BPPARAM = bpparam()
)

Arguments

msexp	MsExperiment object
metrics	character specifying the quality metrics to be calculated on msexp
filterEmptySpectra	logical(1) specifying if empty entries and entries with intensity zero of the Spectra object will be removed
...	arguments passed to the quality metrics functions defined in metrics
BPPARAM	Parallel processing setup. Defaults to BPPARAM = bpparam(). See [bpparam()] for details on parallel processing with BiocParallel.

Details

The metrics are defined by the argument metrics. Further arguments passed to the quality metric functions can be specified by the params argument. params can contain named entries which are matched against the formal arguments of the quality metric functions.

Setting the argument filterEmptySpectra to TRUE will remove zero-length entries, zero-intensity entries, and entries with intensities that are Inf from the Spectra object.

Value

data.frame containing in the columns the metrics for the different spectra (in rows)

Author(s)

Thomas Naake

Examples

library(msdata)
library(MsExperiment)
library(S4Vectors)

msexp <- MsExperiment()
sd <- DataFrame(sample_id = c("QC1", "QC2"),
    sample_name = c("QC Pool", "QC Pool"), injection_idx = c(1, 3))
sampleData(msexp) <- sd

## define file names containing spectra data for the samples and
## add them, along with other arbitrary files to the experiment
fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
experimentFiles(msexp) <- MsExperimentFiles(
    mzML_files = fls,
    annotations = "internal_standards.txt")
## link samples to data files: first sample to first file in "mzML_files",
## second sample to second file in "mzML_files"
msexp <- linkSampleData(msexp, with = "experimentFiles.mzML_files",
    sampleIndex = c(1, 2), withIndex = c(1, 2))
msexp <- linkSampleData(msexp, with = "experimentFiles.annotations",
     sampleIndex = c(1, 2), withIndex = c(1, 1))

library(Spectra)
## import the data and add it to the mse object
spectra(msexp) <- Spectra(fls, backend = MsBackendMzR())

## define the quality metrics to be calculated
metrics <- c("areaUnderTic", "chromatographyDuration", "msSignal10xChange")

## additional parameters passed to the quality metrics functions
## (msLevel is an argument of areaUnderTic and msSignal10xChange,
## relativeTo is an argument of msSignal10xChange) passed to ...
calculateMetricsFromMsExperiment(msexp = msexp, metrics = metrics,
    msLevel = 1, change = "jump", relativeTo = "Q1")

calculateMetricsFromMsExperiment(msexp = msexp, metrics = metrics, 
    msLevel = 1, change = "fall", relativeTo = "previous")

tnaake/MsQuality documentation built on Jan. 30, 2025, 5:24 a.m.