View source: R/function_calculateMetrics_from_Spectra.R
calculateMetricsFromSpectra | R Documentation |
The function calculateMetricsFromSpectra
calculates quality metrics
from a Spectra
object. The function will calculate the
metrics per sample according to the grouping parameter f
,
e.g. dataOrigin
information.
calculateMetricsFromSpectra( spectra, metrics = qualityMetrics(spectra), f = spectra$dataOrigin, ... )
spectra |
|
metrics |
|
f |
|
... |
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
argument. 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, thomasnaake@googlemail.com
library(msdata) library(Spectra) ## define file names containing spectra data for the samples fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE) ## import the data and add it to the spectra object 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 ... calculateMetricsFromSpectra(spectra = spectra, metrics = metrics, msLevel = 1, change = "jump", relativeTo = "Q1") calculateMetricsFromSpectra(spectra = spectra, metrics = metrics, msLevel = 1, change = "fall", relativeTo = "previous")
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