calculateMetrics: Calculate QC metrics from a Spectra or MsExperiment object

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

Description

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

Usage

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

Arguments

object	'Spectra' or 'MsExperiment' object
metrics	'character' specifying the quality metrics to be calculated on 'mse'
...	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

named 'numeric' vector (if 'object' is a 'Spectra' object) or 'data.frame' containing in the columns the metrics for the different spectra (in rows, if 'object' is a 'MsExperiment' object)

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/MsQuality documentation built on Jan. 14, 2022, 7:34 p.m.