View source: R/function_calculateMetrics_from_Spectra.R
Calculate QC metrics from a
calculateMetrics is a wrapper for the functions
calculateMetrics(object, metrics = qualityMetrics(object), ...)
arguments passed to the quality metrics functions defined in
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 and in rows the samples
Thomas Naake, firstname.lastname@example.org
library(msdata) library(Spectra) fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE) spectra <- Spectra(fls, backend = MsBackendMzR()) ## define the quality metrics to be calculated metrics <- c("areaUnderTic", "rtDuration", "msSignal10xChange") #' ## calculate the metrics ## additional parameters passed to the quality metrics functions ## (MsLevel is an argument of areaUnderTic and msSignal10xChange, ## relativeTo is an argument of msSignal10xChange) passed to ... calculateMetrics(object = spectra, metrics = metrics, msLevel = 1, change = "jump", relativeTo = "Q1") calculateMetrics(object = spectra, metrics = metrics, msLevel = 1, change = "fall", relativeTo = "previous")
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