calculateMetricsFromMsExperiment: Calculate QC metrics from a MsExperiment object

Description Usage Arguments Details Value Author(s) Examples

View source: R/function_calculateMetrics_from_Spectra_or_MsExperiment.R

Description

The function 'calculateMetricsFromMsExperiment' calculates quality metrics from a 'MsExperiment' object. Each spectra in the 'mse' object should refer to one mzML file/to one sample.

Usage

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Arguments

msexp

'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

'data.frame' containing in the columns the metrics for the different spectra (in rows)

Author(s)

Thomas Naake, thomasnaake@googlemail.com

Examples

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library(msdata)
library(MsExperiment)
library(S4Vectors)
mse <- MsExperiment()
sd <- DataFrame(sample_id = c("QC1", "QC2"),
    sample_name = c("QC Pool", "QC Pool"), injection_idx = c(1, 3))
sampleData(mse) <- sd

## define file names containing spectra data for the samples and
## add them, along with other arbitrary files to the experiment
fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
experimentFiles(mse) <- MsExperimentFiles(
    mzML_files = fls,
    annotations = "internal_standards.txt")
## link samples to data files: first sample to first file in "mzML_files",
## second sample to second file in "mzML_files"
mse <- linkSampleData(mse, with = "experimentFiles.mzML_files",
    sampleIndex = c(1, 2), withIndex = c(1, 2))
mse <- linkSampleData(mse, with = "experimentFiles.annotations",
                      sampleIndex = c(1, 2), withIndex = c(1, 1))

library(Spectra)
## import the data and add it to the mse object
spectra(mse) <- 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 ...
calculateMetricsFromMsExperiment(msexp = mse, metrics = metrics, 
    msLevel = 1, change = "jump", relativeTo = "Q1")
calculateMetricsFromMsExperiment(msexp = mse, metrics = metrics, 
    msLevel = 1, change = "fall", relativeTo = "previous")

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