calculateMetrics: Calculate QC metrics from a Spectra or MsExperiment object

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

Calculate QC metrics from a Spectra or MsExperiment object

Description

Calculate QC metrics from a Spectra or MsExperiment object. calculateMetrics is a wrapper for the functions calculateMetricsFromSpectra and calculateMetricsFromMsExperiment.

Usage

calculateMetrics(object, metrics = qualityMetrics(object), ...)

Arguments

object	Spectra or MsExperiment object
metrics	character specifying the quality metrics to be calculated on object
...	arguments passed to the quality metrics functions defined in metrics

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.

Value

data.frame containing in the columns the metrics for the different spectra and in rows the samples

Author(s)

Thomas Naake, [e-mail]

Examples

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")

tnaake/msQC documentation built on March 1, 2023, 8:11 p.m.