makeQCReport,RccSet-method: Make NanoString QC report

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.

Usage

"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.

Examples

Run this code

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

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