View source: R/function_calculateMetrics_from_Spectra.R
calculateMetricsFromMsExperiment calculates quality
metrics from a
MsExperiment object. Each spectra in the
msexp object should refer to one mzML file/to one sample.
calculateMetricsFromMsExperiment( msexp, metrics = qualityMetrics(msexp), ..., BPPARAM = bpparam() )
arguments passed to the quality metrics functions defined in
Parallel processing setup. Defaults to 'BPPARAM = bpparam()'. See [bpparam()] for details on parallel processing with 'BiocParallel'.
The metrics are defined by the argument
metrics. Further arguments
passed to the quality metric functions can be specified by the
params can contain named entries which are matched against
the formal arguments of the quality metric functions.
data.frame containing in the columns the metrics for the
different spectra (in rows)
Thomas Naake, firstname.lastname@example.org
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", "rtDuration", "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")
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