shinyMsQuality: Shiny application to visualize quality metrics

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

Shiny application to visualize quality metrics

Description

The function shinyMsQuality function starts a shiny application to visualize the quality metrics interactively. It allows to display all metrics contained in qc.

The function accepts the output of calculateMetrics, calculateMetricsFromSpectra, or calculateMetricsFromMsExperiment

Usage

shinyMsQuality(qc)

Arguments

qc	matrix, contains the calculated quality metrics, the columns contain the metrics and the rows the samples

Details

The plots within the shiny application can be saved by clicking on the download button.

Value

shiny

Author(s)

Thomas Naake, [e-mail]

Examples

library(msdata)
library(MsExperiment)
library(S4Vectors)
msexp <- MsExperiment()
sd <- DataFrame(sample_id = c("QC1", "QC2"),
    sample_name = c("QC Pool", "QC Pool"), injection_idx = c(1, 3))
sampleData(msexp) <- 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(msexp) <- 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"
msexp <- linkSampleData(msexp, with = "experimentFiles.mzML_files",
    sampleIndex = c(1, 2), withIndex = c(1, 2))
msexp <- linkSampleData(msexp, with = "experimentFiles.annotations",
    sampleIndex = c(1, 2), withIndex = c(1, 1))

library(Spectra)
## import the data and add it to the mse object
spectra(msexp) <- 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)
qc <- calculateMetricsFromMsExperiment(msexp = msexp, metrics = metrics, 
    msLevel = 1, relativeTo = "Q1", change = "jump")
rownames(qc) <- c("Sample 1", "Sample 2")

if (interactive())
    shinyMsQuality(qc = qc)

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