makeQCReport: Make NanoString QC report

In NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data

Description

Creates an html QC report for an RccSet object. Alongside the html file, a directory with matching filename is produced that contains additional files as well as high resolution versions of the various plots in the report. In addition to generating the QC report, the function returns a copy of the input RccSet with columns added to phenoData that show the QC flags for each sample.

The various plots in the report depend upon correct annotation and preprocessing in the input object. If the input is missing any elements required for a given plot, the plot will be replaced with a message indicating the missing elements. If the preprocOverride argument is set to TRUE, the input's preprocessing will be ignored and a default configuration will be used so that all applicable plots will be rendered.

Usage

## S4 method for signature 'RccSet'
makeQCReport(rccSet,
  outputBaseName = "NanoStringQCPro_QC_report", outputDir = getwd(),
  preprocOverride = FALSE,
  experimentTitle = expinfo(experimentData(rccSet))["title"],
  covar = "SampleType", method = c("cutoffByMMAD", "cutoffByVar"),
  stringency = 4, maxMiss = 0.2, sampleNameCol = "SampleID",
  heatmaps = FALSE, cleanMarkdown = TRUE, verbose = FALSE)

Arguments

rccSet	RccSet object for which to generate the QC report.
outputBaseName	Character string specifying the base filename (without extension) to use for the output file.
outputDir	Character string specifying the path to the output directory for the QC report and associated files.
preprocOverride	Logical. If TRUE, the input's preprocessing will be ignored, and a default preprocessing configuration (specifically, the defaults for preprocRccSet()) will be applied so that all applicable plots can be rendered in the report.
experimentTitle	Character string specifying an easy to read identifier of the experiment.
covar	Character string specifying a covariate for stratifying samples (e.g. "SampleType").
method	Method to determine outlier samples: either "cutoffByVar" or "cutoffByMMAD".
stringency	Multiplier with which to adjust cutoff values for determining outlier samples.
maxMiss	Numeric specifying the allowable fraction of genes below the lower limit of detection in a sample.
sampleNameCol	Character string specifying the name of the phenoData column holding the sample names.
heatmaps	Logical: render and show heatmaps?
cleanMarkdown	Logical: upon completion, delete markdown files used to produce QC report?
verbose	Logical: print progress messages?

Value

An html report is written to disk and a copy of the input RccSet is invisibly returned with columns added to phenoData that show the QC flags for each sample.

Author(s)

Dorothee Nickles, Thomas Sandmann, Robert Ziman, Richard Bourgon

Examples

data(example_rccSet)
norm_example_rccSet <- preprocRccSet(example_rccSet)
qc_example_rccSet <- makeQCReport(norm_example_rccSet, "example_QC_report")

NanoStringQCPro documentation built on Nov. 8, 2020, 8:11 p.m.