calculateMetrics: Calculate QC metrics from a Spectra object

View source: R/function_calculateMetrics_from_Spectra.R

calculateMetricsR Documentation

Calculate QC metrics from a Spectra object

Description

Calculate QC metrics from a 'Spectra' object. 'calculateMetrics' is a wrapper for the function 'calculateMetricsFromSpectra'.

Usage

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

Arguments

object

'Spectra' 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 (samples in row)

Author(s)

Thomas Naake, thomasnaake@googlemail.com

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 Dec. 1, 2022, 10:01 p.m.